Molecular markers associated with yellow flash in glyphosate tolerant soybeans

ABSTRACT

The present invention provides methods and compositions for the identification and selection of loci modulating phenotypic expression of a herbicide tolerance trait in plant breeding. In addition, methods are provided for screening germplasm entries for the performance and expression of this trait.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application Ser. No. 61/380,024, filed Sep. 3, 2010 and incorporated herein by reference in its entirety.

INCORPORATION OF SEQUENCE LISTING

A sequence listing containing the file named “46_(—)21_(—)54534.txt” which is 19,743 bytes (measured in MS-Windows®) and created on Aug. 30, 2010, comprises 32 nucleotide sequences, is provided herewith via the USPTO's EFS system and is herein incorporated by reference in its entirety. Also incorporated herein by reference are the 32 nucleotide sequences and pertinent identifying information in the Sequence Listing containing the file named “46_(—)21_(—)54534.txt” which is 18477 bytes (measured in MS-Windows®), created on Aug. 30, 2010, and filed with U.S. Provisional Application Ser. No. 61/380,024 on Sep. 3, 2010.

Incorporation of Table 2

A listing of various soybean linkage group L (chromosome 19) markers is provided herewith in the Specification as Table 2. Also incorporated herein by reference is the listing of various soybean linkage group L (chromosome 19) markers that was provided in the document “Appendix to the Specification as Table 2” that was 4541064 bytes (as measured in MS-Windows®), filed with U.S. Provisional Application Ser. No. 61/380,024 on Sep. 3, 2010. Table 2 appears in the final pages of the specification.

BACKGROUND OF INVENTION

“Yellow Flash” is an undesirable phenotype observed in certain soybean varieties that comprise a transgene that confers tolerance to the broad-spectrum herbicide glyphosate. After application of glyphosate, or applications of glyphosate under certain environmental conditions such as high temperature, the leaves of certain soybean plant varieties comprising the transgene that confers glyphosate tolerance can exhibit a yellowish color (hence, the term “Yellow Flash”). The Yellow Flash phenotype can be observed approximately a week after herbicide application in certain soybean varieties comprising the transgene that confers glyphosate tolerance. The yellow flash phenotype is undesirable as it leads to a visually displeasing off-type yellow leaf color in soybean plants exposed to glyphosate.

SUMMARY OF INVENTION

Although the Yellow Flash phenotype can be observed approximately a week after herbicide application in certain soybean varieties comprising the transgene that confers glyphosate tolerance, distinct soybean varieties that comprise the same glyphosate tolerant transgene integrated at the same chromosomal locus (i.e. the same transgenic event) can show various degrees of yellow flash upon exposure to high doses of glyphosate. Some varieties comprising the glyphosate tolerant transgene insertion are highly resistance to high dosages of glyphosate, showing no yellow flash phenotype (i.e. a “no flash phenotype”), while other varieties comprising the same glyphosate tolerant transgene insertion are highly susceptible to high dosages of glyphosate, showing a severe yellow flash phenotype. Provided herein are soybean plants comprising an introgressed genomic region associated with a no flash phenotype. Also provided herein are markers that reside outside of a genomic region associated with a no flash phenotype and that facilitate breeding activities that include, but are not limited to, introgression of this genomic region. Markers and specific alleles thereof that are associated with a no flash phenotype are also provided. Methods of obtaining a soybean plant that exhibits a no flash phenotype and methods of obtaining a soybean plant comprising in its genome at least one no flash locus are also provided. Methods that provide for the introgression of a genomic region associated with a no flash phenotype into soybean germplasm that has a genomic region associated with a yellow flash phenotype. Identification of molecular markers associated with loci that confer the no flash phenotype has significant economic value. By using markers associated with the no flash trait, breeders can select soybean varieties with the favorable alleles (i.e. alleles that are not associated with the yellow flash trait) for use in trait integration. They can also use the markers to help them eliminate unfavorable alleles (i.e. alleles that are associated with the yellow flash trait) in soybean unfavorable allele. This invention thus provides for commercially desirable transgenic soybean lines that carry a genomic region that is associated with a “no flash” phenotype and tolerate high dosages of glyphosate.

Methods of identifying a soybean plant that comprises a genotype associated with a no flash phenotype are thus provided. In certain embodiments, methods of identifying a soybean plant that comprises a genotype associated with a no flash phenotype, comprising: detecting in the soybean plant an allele in at least one yellow flash marker locus associated with the no flash phenotype wherein the yellow flash marker locus is in a linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO:14), and denoting that the plant comprises a genotype associated with a no flash phenotype. In certain embodiments, the methods further comprise the step of selecting the denoted plant from a population of plants. In certain embodiments of any of the aforementioned methods, the denoted plant comprises a transgene that confers tolerance to glyphosate are provided. In certain embodiments where the denoted plant comprises a transgene that confers tolerance to glyphosate, the soybean plant or progeny thereof is exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety. In certain embodiments of the aforementioned methods, a plant that exhibits a no flash phenotype is selected. In certain embodiments of the aforementioned methods, the genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci TA14086_(—)34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14). In certain embodiments of the aforementioned methods, the genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in the linkage group L region selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7) that is associated with a no flash phenotype.

Also provided are methods for obtaining a soybean plant comprising in its genome at least one no flash locus. In certain embodiments, a method for obtaining a soybean plant comprising in its genome at least one no flash locus, comprising the steps of: a. genotyping a plurality of soybean plants with respect to at least one yellow flash locus in a first linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO:14); and, b. selecting a soybean plant comprising in its genome at least one no flash locus comprising a genotype associated with no flash phenotype are provided. In certain embodiments of these methods, the genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16); and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci TA14086_(—)34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14). In certain embodiments of the aforementioned methods, the genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in the first linkage group L region, the first sub-region, or the second sub-region, wherein the marker is selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7). In certain embodiments, the plurality of soybean plants comprises a population that is obtained by: i) crossing a parent plant comprising at least one no flash locus with a parent plant comprising at least one yellow flash locus; or, ii) obtaining seed or progeny from a parental plant segregating for at least one no flash locus. In certain embodiments, the population contains plants that comprise a transgene that confers tolerance to glyphosate. In certain embodiments, the aforementioned methods can further comprise the step of assaying for the presence of at least one additional marker, wherein the additional marker is either linked or unlinked to the linkage group L genomic region. In certain embodiments of the aforementioned methods, the plurality of soybean plants, the soybean plant, and/or progeny thereof are exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety. In certain embodiments of the aforementioned methods, a plant that exhibits a no flash phenotype is selected.

Also provided herewith are methods for producing a soybean plant comprising in its genome at least one introgressed no flash locus. In certain embodiments, a method for producing a soybean plant comprising in its genome at least one introgressed no flash locus comprising the steps of: a. crossing a first no flash soybean plant with a second soybean plant comprising: a yellow flash locus in a first linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14), and at least one linked polymorphic locus not present in the first no flash soybean plant to obtain a population segregating for the no flash loci and the linked polymorphic locus; b. detecting at least two polymorphic nucleic acids in at least one soybean plant from the population, wherein at least one of the polymorphic nucleic acids is located in the first linkage group L region and wherein at least one of the polymorphic amino acids is a linked polymorphic locus not present in the first no flash soybean plant; and c. selecting a soybean plant comprising a genotype associated with a no flash phenotype and at least one linked marker found in the second soybean plant comprising a yellow flash locus but not in the first no flash soybean plant, thereby obtaining a soybean plant comprising in its genome at least one introgressed no flash locus are provided. In certain embodiments of the methods, at least one of the first or the second soybean plants comprises a transgene that confers tolerance to glyphosate. In certain embodiments of the methods, the population, the selected soybean plant, and/or progeny of selected soybean plant is exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety. In certain embodiments, the yellow flash locus comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16); and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci TA14086_(—)34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14). In certain embodiments of the aforementioned methods, the polymorphic nucleic acid detected in step (b) is detected with at least one marker selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7). In certain embodiments of the aforementioned methods, the polymorphic nucleic acid detected in step (b) is detected with at least one marker selected from the group consisting of M0101742 (SEQ ID NO:5) and M0129925 (SEQ ID NO:7). In certain embodiments of the aforementioned methods, the polymorphic nucleic acids are detected with marker M0101742 (SEQ ID NO:5) and with marker M0129925 (SEQ ID NO:7). In certain embodiments of the aforementioned methods, the linked polymorphic locus is detected with a genotypic marker, a phenotypic marker, or both. In certain embodiments of the methods, the linked polymorphic locus is detected with a marker that is located within about 1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) of the no flash locus. In certain embodiments of the methods, the linked polymorphic locus is detected with at least one marker selected from the group consisting of M0205928 (SEQ ID NO:3), M0205537 (SEQ ID NO:8), M0202715 (SEQ ID NO:9), M0206286 (SEQ ID NO:10), M0206054 (SEQ ID NO:11) and M0205375 (SEQ ID NO:12). Also provided herewith are soybean plants comprising an introgressed no flash locus made by the aforementioned methods. In certain embodiments, a soybean plant comprising an introgressed no flash locus and one or more polymorphic loci comprising alleles or combinations of alleles that are not found in a no flash soybean variety and that are linked to the introgressed no flash locus, wherein the plant is produced by the aforementioned methods are provided.

Also provided are soybean plants comprising an introgressed no flash locus and one or more polymorphic loci comprising alleles or combinations of alleles that are not found in a no flash soybean variety and that are linked to the introgressed no flash locus.

Also provided are substantially purified nucleic acid molecules comprising a nucleic acid molecule selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7), or a fragment thereof that contains a specific allelic variant of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), or M0129925 (SEQ ID NO:7). In certain embodiments, the fragment that contains the allelic variant is at least 15, at least 18, at least 20, at least 22, at least 25, or at least 30 nucleotides in length.

In certain embodiments, methods for obtaining a soybean plant that exhibits a no flash phenotype comprising the steps of: a) crossing a soybean plant that exhibits a no flash phenotype with a soybean plant that exhibits a yellow flash phenotype, wherein at least one of the soybean plants comprises a transgene that confers tolerance to glyphosate, and b) selecting a progeny plant from the cross, wherein the progeny plant comprises the transgene that confers glyphosate tolerance and wherein the progeny plant exhibits a no flash phenotype are provided. In certain embodiments of the methods, the selection in step b can comprise: i) genotyping the progeny plant with respect to a yellow flash locus in a linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14); and/or ii) exposing the progeny plant to glyphosate and scoring the plant for a no flash phenotype. In certain embodiments of the methods, a soybean plant that exhibits a yellow flash phenotype comprises at least one linked or unlinked marker not present in the first no flash soybean plant. In certain embodiments, the progeny plant is further selected for the presence of the linked or unlinked marker.

Also provided are methods of breeding soybean plants comprising the steps of: a. selecting a first soybean plant comprising a genotype in the linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) that is associated with a no flash phenotype from a population of soybean plants that is segregating for the genotype; and, b) crossing the selected soybean plant with a second soybean plant. In certain embodiments of these methods, one or both of the soybean plants comprises a transgene that confers glyphosate tolerance.

Further areas of applicability will become apparent from the description provided herein. It should be understood that the description and specific examples are intended for purposes of illustration only and are not intended to limit the scope of the present disclosure.

DETAILED DESCRIPTION OF INVENTION I. Definition

As used herein, an “allele” refers to one of two or more alternative forms of a genomic sequence at a given locus on a chromosome. When all the alleles present at a given locus on a chromosome are the same, that plant is homozygous at that locus. If the alleles present at a given locus on a chromosome differ, that plant is heterozygous at that locus.

As used herein, the term “denoting” when used in reference to a plant genotype refers to any method whereby a plant is indicated to have a certain genotype. Such indications of a certain genotype include, but are not limited to, any method where a plant is physically marked or tagged. Physical markings or tags that can be used include, but not limited to, a barcode, a radio-frequency identification (RFID), a label or the like. Indications of a certain genotype also include, but are not limited to, any entry into any type of written or electronic database whereby the plant's genotype is provided.

A “locus” is a position on a genomic sequence that is usually found by a point of reference; e.g., a short DNA sequence that is a gene, or part of a gene or intergenic region. A locus may refer to a nucleotide position at a reference point on a chromosome, such as a position from the end of the chromosome.

As used herein, “linkage group L” corresponds to the soybean linkage group L described in Choi, et al., Genetics. 2007 May; 176(1): 685-696. Linkage group L, as used herein, also corresponds to soybean chromosome 19 (as described on the World Wide Web at soybase.org/LG2Xsome.php). As used herein, “polymorphism” means the presence of one or more variations of a nucleic acid sequence at one or more loci in a population of at least two members. The variation can comprise but is not limited to one or more nucleotide base substitutions, the insertion of one or more nucleotides, a nucleotide sequence inversion, and/or the deletion of one or more nucleotides.

As used herein, the term “single nucleotide polymorphism,” also referred to by the abbreviation “SNP,” means a polymorphism at a single site wherein the polymorphism constitutes any or all of a single base pair change, an insertion of one or more base pairs, and/or a deletion of one or more base pairs.

As used herein, “marker” means a detectable characteristic that can be used to discriminate between organisms. Examples of such characteristics include, but are not limited to, genetic markers, biochemical markers, fermentation yield, fermentation efficiency, energy yield, secondary compounds, metabolites, morphological characteristics, and agronomic characteristics.

As used herein, “marker assay” means a method for detecting a polymorphism at a particular locus using a particular method. Marker assays thus include, but are not limited to, measurement of at least one phenotype (such as seed color, flower color, or other visually detectable trait as well as any biochemical trait), restriction fragment length polymorphism (RFLP), single base extension, electrophoresis, sequence alignment, allelic specific oligonucleotide hybridization (ASO), random amplified polymorphic DNA (RAPD), microarray-based polymorphism detection technologies, and the like.

As used herein, “genotype” means the genetic component of the phenotype and it can be indirectly characterized using markers or directly characterized by nucleic acid sequencing.

As used herein, the term “introgressed”, when used in reference to a genetic locus, refers to a genetic locus that has been introduced into a new genetic background. Introgression of a genetic locus can thus be achieved through both plant breeding methods or by molecular genetic methods. Such molecular genetic methods include, but are not limited to, various plant transformation techniques and/or methods that provide for homologous recombination, non-homologous recombination, site-specific recombination, and/or genomic modifications that provide for locus substitution or locus conversion. In certain embodiments, introgression could thus be achieved by substitution of a yellow flash locus with a corresponding no flash locus or by conversion of a locus from a yellow flash genotype to a no flash genotype.

As used herein, “phenotype” means the detectable characteristics of a cell or organism which can be influenced by gene expression.

As used herein, “linkage” refers to relative frequency at which types of gametes are produced in a cross. For example, if locus A has genes “A” or “a” and locus B has genes “B” or “b” and a cross between parent I with AABB and parent B with aabb will produce four possible gametes where the genes are segregated into AB, Ab, aB and ab. The null expectation is that there will be independent equal segregation into each of the four possible genotypes, i.e. with no linkage ¼ of the gametes will of each genotype. Segregation of gametes into a genotypes differing from ¼ are attributed to linkage.

As used herein, the termed “linked”, when used in the context of markers and/or genomic regions, means that the markers and/or genomic regions are located on the same linkage group or chromosome.

As used herein, a “nucleic acid molecule,” be it a naturally occurring molecule or otherwise may be “substantially purified”, if desired, referring to a molecule separated from substantially all other molecules normally associated with it in its native state. More preferably, a substantially purified molecule is the predominant species present in a preparation. A substantially purified molecule may be at least about 60% free, preferably at least about 75% free, more preferably at least about 90% free, and most preferably at least about 95% free from the other molecules (exclusive of solvent) present in the natural mixture. The term “substantially purified” is not intended to encompass molecules present in their native state.

As used herein, “quantitative trait locus (QTL)” means a locus that controls to some degree numerically representable traits that are usually continuously distributed. As used herein, the term “transgene” means nucleic acid molecules in the form of DNA, such as cDNA or genomic DNA, and RNA, such as mRNA or microRNA, which may be single or double stranded.

As used herein, the term “event”, when used in the context of describing a transgenic plant, refers to a particular transformed plant line. In a typical transgenic breeding program, a transformation construct responsible for a trait is introduced into the genome via a transformation method. Numerous independent transformants (events) are usually generated for each construct. These events are evaluated to select those with superior performance.

As used herein, the term “soybean” means Glycine max and includes all plant varieties that can be bred with soybean, including wild soybean species. In certain embodiments, soybean plants from the species Glycine max and the subspecies Glycine max L. ssp. max or Glycine max ssp. formosana can be genotyped using the compositions and methods of the present invention. In an additional aspect, the soybean plant is from the species Glycine soja, otherwise known as wild soybean, can be genotyped using these compositions and methods. Alternatively, soybean germplasm derived from any of Glycine max, Glycine max L. ssp. max, Glycine max ssp. Formosana, and/or Glycine soja can be genotyped using compositions and methods provided herein.

As used herein, the term “bulk” refers to a method of managing a segregating population during inbreeding that involves growing the population in a bulk plot, harvesting the self pollinated seed of plants in bulk, and using a sample of the bulk to plant the next generation

As used herein, the phrase “Single Plant Selection” (or the acronym “SPS”) refers to a method that is often used instead of bulk method (see immediately above) to advance segregating germplasm in early generations. SPS is always used to advance germplasm to “Progeny Row” (Prow) and “Progeny Row Yield Trial” (PRYT) analyses.

As used herein, the phrase “Progeny Row” (Prow) refers to a plant breeding and analysis method where a row of progeny plants from SPS is grown for observation, further selection, and/or bulking

As used herein, the phrase “Progeny Row Yield Trial” (PRYT) refers to a plant breeding and analysis method where a row of plants from a SPS is grown in a small yield trial with other SPS material. In most instances, the PRYT is usually from the same population and usually consists of one rep at one location.

As used herein, the term “comprising” means “including but not limited to”.

II. Description of the Invention Overview

In accordance with the present invention, Applicants have discovered genomic regions, associated markers, and associated methods for identifying and associating genotypes that effect a transgene-mediated glyphosate tolerance trait. For example, in one embodiment, a method of the invention comprises screening a plurality of transgenic germplasm entries displaying a heritable variation for at least one transgene mediated glyphosate tolerance trait wherein the heritable variation is linked to at least one genotype; and associating at least one genotype from the transgenic germplasm entries to at least one transgene mediated glyphosate tolerance trait. In another embodiment, a method of the invention comprises crossing at least two germplasm entries with a test germplasm entry for the evaluation of performance of at least one transgene mediated glyphosate tolerance trait in order to determine preferred crossing schemes. The methods of the present invention can be used with traditional breeding techniques as described below to more efficiently screen and identify genotypes affecting a transgene-mediated glyphosate tolerance trait.

The use of markers to infer a phenotype of interest results in the economization of a breeding program by substituting costly, time-intensive phenotyping assays with genotyping assays. Further, breeding programs can be designed to explicitly drive the frequency of specific, favorable phenotypes by targeting particular genotypes (U.S. Pat. No. 6,399,855). Fidelity of these associations may be monitored continuously to ensure maintained predictive ability and, thus, informed breeding decisions (US Patent Application 2005/0015827). In this case, costly, time-intensive phenotyping assays required for determining if a plant or plants contains a genomic region associated with a “no flash” or “yellow flash” phenotype can be supplanted by genotypic assays that provide for identification of a plant or plants that contain the desired genomic region.

III. A Genomic Region Associated with a No Flash Phenotype

Provided herewith is a soybean genomic region that is shown herein to be associated with a desirable no flash phenotype when present in certain allelic forms and when combined with certain transgenic loci that confer glyphosate tolerance.

A soybean genomic region provided that can be associated with a desirable no flash phenotype when present in certain allelic forms is located on the telomere proximal end of the short arm of soybean linkage group L (chromosome 19). A series of markers useful in practicing the methods of this invention are provided herewith in Table 1. Additional markers useful in the practice of the invention are provided herewith in Table 2 of the Specification, which is incorporated herewith by reference in its entirety. Table 2 provides the Table 1 markers, additional nucleic acid markers or loci that have been disclosed in various databases, the relative positions of the markers on a physical map of linkage group L (soybean chromosome 19), and sources for the markers.

TABLE 1 Markers spanning a genomic region associated with a desirable no flash phenotype SEQ Allelic form(s) Marker or ID Map Associated with No Locus Name NO: Position¹ Flash Phenotype² M0205350 1 423935 M0114388 2 380897 M0205928 3 92526 M0129138³ 4 114013 GG⁷ or AA⁸ M0101742⁴ 5 112836 TT⁷ or CC⁸ M0093116⁵ 6 805580 AA⁷ or TT⁸ M0129925⁶ 7 831128 CC⁷ or GG^(7,8) M0205537 8 890254 M0202715 9 921431 M0206286 10 1209977 M0206054 11 1465354 M0205375 12 2009800 BG406195 13 107207 BU082700 14 864145 ¹The relative positions of the middle position of the listed markers or loci based on nucleotide positions on a physical map of soybean linkage group L (chromosome 19) of Table 2 are provided where nucleotide position 0 (zero) is telomere proximal and nucleotide position 2009800 is centromere proximal. Polymorphic nucleotide bases are designated in the sequence listing provided herewith according to the WIPO Standard ST.25 (1998), Table 1, as follows: r = g or a (purine); y = t/u or c (pyrimidine); m = a or c; (amino); k = g or t/u (keto); s = g or c (strong interactions 3 H-bonds); w = a or t/u (weak interactions 2H-bonds); b = g or c or t/u (not a); d = a or g or t/u (not c); h = a or c or t/u (not g); v = a or g or c (not t, not u); and n = a or g or c or t/u (unknown, or other; any.) ²Both the maternal and paternal alleles of the single nucleotide polymorphisms that can be associated with a non flash phenotype are shown. ³The identified polymorphic allele of marker M0129138 is located at nucleotide 218 of SEQ ID NO: 4. ⁴The identified polymorphic allele of marker M0101742 is located at nucleotide 1206 of SEQ ID NO: 5. ⁵The identified polymorphic allele of marker M0093116 is located at nucleotide 183 of SEQ ID NO: 6. ⁶The identified polymorphic allele of marker M0129925 is located at nucleotide 328 of SEQ ID NO: 7. ⁷The identified polymorphic allele of marker M0129138 “GG” can be associated with a no flash phenotype when the identified polymorphic alleles of the other markers are: “TT” for M0101742, “AA” for marker M0093116, and either “GG” or “CC” for marker M0129925. ⁸The identified polymorphic allele of marker M0129138 “AA” can be associated with a no flash phenotype when the identified polymorphic alleles of the other markers are: “CC” for M0101742, “TT” for marker M0093116, and “GG” for marker M0129925.

Also provided herein are sub-regions of the linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID: 14) that are associated with a no flash phenotype. A first sub-region of the linkage group L region associated with a no flash phenotype is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16). These loci flank a first sub-region that spans telomere proximal nucleotide 107039 to centromere proximal nucleotide 115956 in the physical map of linkage group L provided in Table 2 of the specification. Polymorphisms located in this first sub-region that are associated with a no flash phenotype can be detected with markers that include, but are not limited to, M0129138 (SEQ ID NO: 4) and M0101742 (SEQ ID NO: 5). A second sub-region of the linkage group L region associated with a no flash phenotype is flanked by loci TA14086_(—)34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14). These loci flank the second sub-region that spans telomere proximal nucleotide 800932 to centromere proximal nucleotide 864449 in the physical map of linkage group L provided in Table 2 of the specification. Polymorphisms located in this second sub-region that are associated with a no flash phenotype can be detected with markers that include, but are not limited to, M0093116 (SEQ ID NO: 6), and M0129925 (SEQ ID NO: 7). In certain embodiments of invention, a polymorphism associated with a no-flash phenotype is detected in only one of these sub-regions. In other embodiments of the invention, at least one polymorphism associated with a no-flash phenotype is detected in both of these sub-regions. Thus, one or more markers selected from the group consisting of M0129138 (SEQ ID NO: 4), M0101742 (SEQ ID NO: 5), and markers located between loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16) can be used either independently of, or in combination with, one or more markers selected from the group consisting of M0093116 (SEQ ID NO: 6), and M0129925 (SEQ ID NO: 7), and markers located between loci TA14086_(—)34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14) to detect polymorphisms associated with a no flash phenotype. Conversely, one or more markers selected from the group consisting of M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7), and markers located between loci TA14086_(—)34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14) can also be used independently of, or in combination with, any markers located in the first sub-region to detect polymorphisms associated with a no flash phenotype. In certain embodiments, a polymorphism in the first sub-region is detected with marker M0101742 (SEQ ID NO: 5) and a polymorphism in the second sub-region is detected with marker M0129925 (SEQ ID NO: 7).

Additional genetic markers can be used either in conjunction with the markers provided in Table 1 and/or Table 2 or independently of the markers provided in Table 1 and/or Table 2 to practice the methods of the instant invention. Publicly available marker databases from which useful markers can be obtained include, but are not limited to, the soybase.org website on the internet (World Wide Web) that is administered by the United States Agricultural Research Service, the United States Department of Agriculture, and Iowa State University. Additional soybean markers that can be used and that have been described in the literature include, but are not limited to, Hyten et al., BMC Genomics. 11:38, 2010; Choi et al., Genetics. 176(1):685-96, 2007; Yoon et al., Theor Appl Genet. 2007 March; 114(5):885-99; and Hyten et al. Crop Sci. 2010 50: 960-968. Given the provision herein of a genomic region on linkage group L (chromosome 19) delimited or flanked by the telomere proximal locus BG406195 (SEQ ID NO: 13) of Table 2 and the centromere proximal locus BU082700 (SEQ ID NO: 14) of Table 2 as well as an assortment of soybean germplasms exhibiting either a “yellow-flash” or “no flash” phenotype, additional markers located either within or near this genomic region that are associated with these phenotypes can be obtained by merely typing the new markers in the various germplasms provided herewith. The genomic region on linkage group L (chromosome 19) delimited or flanked by the telomere proximal locus BG406195 (SEQ ID NO: 13) of Table 2 and the centromere proximal locus BU082700 (SEQ ID NO: 14) of Table 2 can also be mapped relative to markers provided in any publicly available or other soybean physical or genetic map to place this genetic locus on that map.

IV. Identification of Plants Exhibiting the “Flash” or “No-Flash” Phenotype

To observe the presence or absence of the “Yellow Flash” or no flash phenotypes, transgenic soybean plants comprising a transgene that confers glyphosate tolerance are typically exposed in early to mid-vegetative growth stages to one or more high doses of glyphosate. Typical doses of glyphosate that can elicit a yellow flash phenotype can range from about a 2-fold label application rate of a commercially available glyphosate formulation to about a 3-fold label application rate of a commercially available glyphosate formulation. In terms of acid equivalents of glyphosate acid applied, typical doses of glyphosate that can elicit a yellow flash phenotype can range from an application rate of about 1.5 pounds of acid equivalent per acre (about 1.68 kilograms per hectare) of glyphosate acid to about 2.25 pounds of acid equivalent per acre (i.e. about 2.52 kilograms per hectare) of glyphosate acid when the indicated amounts of glyphosate acid are provided in either a commercially available glyphosate formulation or when the indicated amounts of glyphosate acid is provided in a similar formulation suitable for application to glyphosate-tolerant crops. Commercially available glyphosate formulations that can be used include, but are not limited to, ROUNDUP ORIGINAL MAX®, ROUNDUP POWERMAX®, ROUNDUP ULTRAMAX®, or ROUNDUP WEATHERMAX® (Monsanto Co., St. Louis, Mo., USA); TOUCHDOWN IQ® or TOUCHDOWN TOTAL® (Syngenta, Wilmington, Del., USA); GLYPHOMAX®, GLYPHOMAX PLUS®, or GLYPHOMAX XRT® (Dow Agrosciences LLC, Indianapolis, Ind., USA) glyphosate formulations. In certain embodiments, the commercially available glyphosate formulation used is ROUNDUP WEATHERMAX®. In certain embodiments, doses of glyphosate that can elicit a yellow flash phenotype can range from about a 2 fold application rate of about 42.6 ounces per acre ROUNDUP WEATHERMAX® (1.68 kilograms per hectare) to about a three fold application rate of about 63.9 ounces per acre ROUNDUP WEATHERMAX® (i.e. about 2.52 kilograms per hectare) glyphosate formulation.

The Yellow Flash phenotype can be observed approximately a week after herbicide application in certain soybean varieties comprising the transgene that confers glyphosate tolerance. Glyphosate is typically applied during vegetative growth stages. In certain embodiments of these methods, glyphosate can be applied in weekly intervals (i.e. once a week) for any of 2, 3, 4 or more successive weeks to score for the presence of the yellow flash phenotype. In certain embodiments, soybean plants at about the V3-V4 vegetative development stage are exposed to an initial glyphosate spray followed by three subsequent sprays at weekly intervals. The first spray can be based on stage of growth and remaining sprays were scheduled at 7 day intervals following initial spray. As discussed herein, the vegetative stages of soybean are as follows: VE (emergence), VC (cotyledon stage), V1 (first trifoliolate leaf), V2 (second trifoliolate leaf), V3 (third trifoliolate leaf), V(n) (nth trifoliolate leaf), and V6 (flowering will soon start). A description of the soybean vegetative stages can be found on the world wide web (internet) at ag.ndsu.edu/pubs/plantsci/rowcrops/a1174/a1174w.htm (North Dakota State University publication A-1174, June 1999, Reviewed and Reprinted August 2004). Expression of the yellow flash trait can also be influenced by temperature, where the trait in varieties that display the yellow flash phenotype is more pronounced following treatment at temperatures of about 32 degrees Celsius or more.

A rating scale that evaluates the degree of yellow flash can also be employed to identify “flash” and “no flash” plants. An exemplary and non limiting scale for evaluating the yellow flash phenotype is as follows, where the low numbers correspond to a “no flash” phenotype and the high numbers correlate to a “flash” phenotype:

1: Green—No Yellowing

2: Mostly green, very slight yellowing <5% (1-2 plants with some yellowing)

3: 5-10% plants with yellowing

4: 11-20% plants with yellowing

5: 21-35% plants with yellowing

6: 36-50% plants with yellowing

7: 51-65% plants with yellowing

8: 66-80% plants with yellowing, some necrosis

9: 81-100% plants with yellowing and or necrosis

V. Introgression of a Genomic Region Associated with a No Flash Phenotype

Also provided herewith are unique soybean germplasm comprising an introgressed genomic region that is associated with a no flash phenotype and methods of obtaining the same. Marker-assisted introgression involves the transfer of a chromosomal region, defined by one or more markers, from one germplasm to a second germplasm. Offspring of a cross that contain the introgressed genomic region can be identified by the combination of markers characteristic of the desired introgressed genomic region from a first germplasm (i.e. such as a no flash germplasm) and both linked and unlinked markers characteristic of the desired genetic background of a second germplasm (i.e. a yellow flash germplasm). In addition to the markers provided herewith that identify alleles of genomic region that is associated with a no flash phenotype, flanking markers that fall on both the telomere proximal end of the genomic region on linkage group L (chromosome 19) and the centromere proximal end of the linkage group L (chromosome 19) genomic region are also provided in Tables 1 and 2. Such flanking markers are useful in a variety of breeding efforts that include, but are not limited to, introgression of the genomic region associated with a no flash phenotype into a genetic background comprising markers associated with germplasm that ordinarily contains the allelic forms of the genomic region that is associated with a “yellow flash” phenotype. Telomere proximal flanking markers that can be used in these methods include, but are not limited to, M0205928 (SEQ ID NO: 3) and/or polymorphisms in any of the loci listed in Table 2 of the Specification located between starting base 16426 (the telomere proximal base) of locus asmbl_(—)11856 and starting base 107039 of locus BG406195. Such polymorphisms can be identified by sequencing loci from flash and no flash germplasms. Centromere proximal flanking markers that can be used in these methods include, but are not limited to, M0202715 (SEQ ID NO: 9), M0206286 (SEQ ID NO: 10), M0206054 (SEQ ID NO: 11), and M0205375 (SEQ ID NO: 12). Additional markers located on linkage group L (chromosome 19) and other chromosomes are disclosed in US Patent Application Publication 20090208964. Publicly available marker databases from which additional useful markers located on linkage group L (chromosome 19) and other chromosomes can be obtained include, but are not limited to, the soybase.org website on the internet that is administered by the United States Agricultural Research Service, the United States Department of Agriculture, and Iowa State University. Soybean plants or germplasm comprising an introgressed genomic region that is associated with a no flash phenotype wherein at least 10%, 25%, 50%, 75%, 90%, or 99% of the remain genomic sequences carry markers characteristic of soybean plants or germplasm that are otherwise or ordinarily comprise a genomic region associated with the yellow flash phenotype are thus provided.

VI. Soybean Plants Comprising Genomic Region Associated with the Flash and No Flash Phenotypes and Transgenes that Confer Tolerance to Glyphosate

A non-limiting and exemplary list of soybean plants that comprise genomic regions associated with either a flash or a no flash phenotype are provided herewith in Table 3.

TABLE 3 Soybean varieties comprising a genomic region associated with a no flash or flash phenotype. ATCC Depository Branded U.S. Pat. Variety Name Accession Name¹ Phenotype No. in Patent Number² AG4201 Flash 7,071,388 SE71112 PTA-5728 AG4601 Flash 5,659,116 927113675 97556. AG4603 Flash 7,067,723 SE73753 PTA-5730 AG4702 Flash 5,750,857 9390369478967 209547 AG4902 Flash 6,143,953 931474956907 PTA-2214 DKB31-51 Flash 6,346,658 950045734453 PTA-3871 DKB37-51 Flash 7,294,764 SD82997 PTA-5737 DKB38-52 Flash 6,660,912 SD92955 PTA-5382 DKB40-51 Flash 6,683,233 SD93038 PTA-5329 DKB46-51 Flash 6,933,423 SE73090 PTA-5733 AG0801 Non-Flash 6,005,170 9422009600716 PTA-269 AG0803 Non-Flash 7,498,489 4498438 PTA-9064 AG0901 Non-Flash 6,080,917 942193611352 203207 AG2403 Non-Flash 6,900,372 SN71173 PTA-5727 AG2603 Non-Flash 7,388,131 4599695 PTA-9070 AG2703 Non-Flash 6,184,442 9323265446452 PTA-2577 AG3006 Non-Flash 7,482,516 0387907 PTA-9029 AG3302 Non-Flash 5,973,235 943470629664 203939 AG3505 Non-Flash 7,569,750 4559809 PTA-9023 AG3703 Non-Flash 6,881,879 SW90702 PTA-5738 AG3903 Non-Flash 6,632,982 SW84112 PTA-5299 AG4403 Non-Flash 6,348,644 9472569612611 PTA-3870 AG4503 Non-Flash 7,378,578 0358232 PTA-9003 AG4703 Non-Flash 7,554,014 437973 PTA-9066 DKB06-51 Non-Flash 6,143,953 931474956907 PTA-2214 DKB08-51 Non-Flash 7,504,565 4878185 PTA-9702 DKB22-52 Non-Flash 6,858,783 0491727 PTA-6187 DKB29-51 Non-Flash 6,884,927 0509249 PTA 6272 DKB42-51 Non-Flash 7,479,582 4671685 PTA-9027 ¹Branded names of ASGROW ® (designated “AG”) and DEKALB ® soybean varieties from Monsanto Co. 800 N. Lindbergh Blvd., St. Louis, MO, USA. ²Deposit numbers of seed available through the American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, Va., USA, 20110-2209.

Also provided herewith are additional soybean plants that comprising a genomic region associated with a flash or no flash phenotype that are identified by use of the markers provided in Table 1 and/or Table 2 and/or methods provided herein. Any of the soybean plants identified in Table 3 or other soybean plants that are otherwise identified using the markers or methods provided herein can be used in methods that include, but are not limited to, methods of obtaining soybean plants with an introgressed no flash locus, obtaining a soybean plant that exhibits a no flash phenotype, or obtaining a soybean plant comprising in its genome a genetic region associated with a no flash phenotype.

In certain embodiments, the soybean plants provided herein or used in the methods provided herein can comprise a transgene that confers tolerance to glyphosate. Transgenes that can confer tolerance to glyphosate include, but are not limited to, transgenes that encode glyphosate tolerant Class I EPSPS (5-enolpyruvylshikimate-3-phosphate synthases) enzymes or glyphosate tolerant Class II EPSPS (5-enolpyruvylshikimate-3-phosphate synthases) enzymes. Useful glyphosate tolerant EPSPS enzymes provided herein are disclosed in U.S. Pat. No. 6,803,501, RE39,247, U.S. Pat. No. 6,225,114, U.S. Pat. No. 5,188,642, and U.S. Pat. No. 4,971,908. In certain embodiments, the glyphosate tolerant soybean plants can comprise a transgene encoding a glyphosate oxidoreductase or other enzyme which degrades glyphosate. Glyphosate oxidoreductase enzymes had been described in U.S. Pat. No. 5,776,760 and U.S. Reissue Pat. RE38,825. In certain embodiments the soybean plant can comprise a transgene encoding a glyphosate N-acetyltransferase gene that confers tolerance to glyphosate. In certain embodiments, the soybean plant can comprise a glyphosate n-acetyltransferase encoding transgene such as those described in U.S. Pat. No. 7,666,644. In still other embodiments, soybean plants comprising combinations of transgenes that confer glyphosate tolerance are provided. Soybean plants comprising both a glyphosate resistant EPSPS and a glyphosate N-acetyltransferase are also provided herewith. In certain embodiments, it is contemplated that the soybean plants used herein can comprise one or more specific genomic insertion(s) of a glyphosate tolerant transgene including, but not limited to, as those found in: i) MON89788 soybean (deposited under ATCC accession number PTA-6708 and described in US Patent Application Publication Number 20100099859), ii) GTS 40-3-2 soybean (Padgette et al., Crop Sci. 35: 1451-1461, 1995), iii) event 3560.4.3.5 soybean (seed deposited under ATCC accession number PTA-8287 and described in US Patent Publication 20090036308), or any combination of i (MON89788 soybean), ii (GTS 40-3-2 soybean), and iii (event 3560.4.3.5 soybean).

In certain embodiments, it is contemplated that genotypic assays that provide for non-destructive identification of the plant or plants can be performed either in seed, the emergence stage, the “VC” stage (i.e. cotyledons unfolded), the V1 stage (appearance of first node and unifoliate leaves), the V2 stage (appearance of the first trifoliate leaf), and thereafter. In certain embodiments, non-destructive genotypic assays are performed in seed using apparati and associated methods as described in U.S. Pat. Nos. 6,959,617; 7,134,351; 7,454,989; 7,502,113; 7,591,101; 7,611,842; and 7,685,768, which are incorporated herein by reference in their entireties. In certain embodiments, non-destructive genotypic assays are performed in seed using apparati and associated methods as described in US Patent Application Publications 20100086963, 20090215060, and 20090025288, which are incorporated herein by reference in their entireties. Published U.S. Patent Applications US 2006/0042527, US 2006/0046244, US 2006/0046264, US 2006/0048247, US 2006/0048248, US 2007/0204366, and US 2007/0207485, which are incorporated herein by reference in their entirety, also disclose apparatus and systems for the automated sampling of seeds as well as methods of sampling, testing and bulking seeds. Thus, in a certain embodiments, any of the methods provided herein can comprise screening for markers in individual seeds of a population wherein only seed with at least one genotype of interest is advanced.

VII. Molecular Assisted Breeding Techniques

Genetic markers that can be used in the practice of the instant invention include, but are not limited to, are Restriction Fragment Length Polymorphisms (RFLP), Amplified Fragment Length Polymorphisms (AFLP), Simple Sequence Repeats (SSR), Single Nucleotide Polymorphisms (SNP), Insertion/Deletion Polymorphisms (Indels), Variable Number Tandem Repeats (VNTR), and Random Amplified Polymorphic DNA (RAPD), and others known to those skilled in the art. Marker discovery and development in crops provides the initial framework for applications to marker-assisted breeding activities (US Patent Applications 2005/0204780, 2005/0216545, 2005/0218305, and 2006/00504538). The resulting “genetic map” is the representation of the relative position of characterized loci (DNA markers or any other locus for which alleles can be identified) along the chromosomes. The measure of distance on this map is relative to the frequency of crossover events between sister chromatids at meiosis.

As a set, polymorphic markers serve as a useful tool for fingerprinting plants to inform the degree of identity of lines or varieties (U.S. Pat. No. 6,207,367). These markers form the basis for determining associations with phenotype and can be used to drive genetic gain. The implementation of marker-assisted selection is dependent on the ability to detect underlying genetic differences between individuals.

Certain genetic markers for use in the present invention include “dominant” or “codominant” markers. “Codominant markers” reveal the presence of two or more alleles (two per diploid individual). “Dominant markers” reveal the presence of only a single allele. The presence of the dominant marker phenotype (e.g., a band of DNA) is an indication that one allele is present in either the homozygous or heterozygous condition. The absence of the dominant marker phenotype (e.g., absence of a DNA band) is merely evidence that “some other” undefined allele is present. In the case of populations where individuals are predominantly homozygous and loci are predominantly dimorphic, dominant and codominant markers can be equally valuable. As populations become more heterozygous and multiallelic, codominant markers often become more informative of the genotype than dominant markers.

In another embodiment, markers that include. but are not limited, to single sequence repeat markers (SSR), AFLP markers, RFLP markers, RAPD markers, phenotypic markers, isozyme markers, single nucleotide polymorphisms (SNPs), insertions or deletions (Indels), single feature polymorphisms (SFPs, for example, as described in Borevitz et al. 2003 Gen. Res. 13:513-523), microarray transcription profiles, DNA-derived sequences, and RNA-derived sequences that are genetically linked to or correlated with no flash loci, regions flanking no flash loci, regions linked to no flash loci, and/or regions that are unlinked to no flash loci can be used in certain embodiments of the instant invention.

In one embodiment, nucleic acid-based analyses for determining the presence or absence of the genetic polymorphism (i.e. for genotyping) can be used for the selection of seeds in a breeding population. A wide variety of genetic markers for the analysis of genetic polymorphisms are available and known to those of skill in the art. The analysis may be used to select for genes, portions of genes, QTL, alleles, or genomic regions (Genotypes) that comprise or are linked to a genetic marker that is linked to or correlated with no flash loci, regions flanking no flash loci, regions linked to no flash loci, and/or regions that are unlinked to no flash loci can be used in certain embodiments of the instant invention.

Herein, nucleic acid analysis methods include, but are not limited to, PCR-based detection methods (for example, TaqMan assays), microarray methods, mass spectrometry-based methods and/or nucleic acid sequencing methods. In one embodiment, the detection of polymorphic sites in a sample of DNA, RNA, or cDNA may be facilitated through the use of nucleic acid amplification methods. Such methods specifically increase the concentration of polynucleotides that span the polymorphic site, or include that site and sequences located either distal or proximal to it. Such amplified molecules can be readily detected by gel electrophoresis, fluorescence detection methods, or other means.

A method of achieving such amplification employs the polymerase chain reaction (PCR) (Mullis et al. 1986 Cold Spring Harbor Symp. Quant. Biol. 51:263-273; European Patent 50,424; European Patent 84,796; European Patent 258,017; European Patent 237,362; European Patent 201,184; U.S. Pat. No. 4,683,202; U.S. Pat. No. 4,582,788; and U.S. Pat. No. 4,683,194), using primer pairs that are capable of hybridizing to the proximal sequences that define a polymorphism in its double-stranded form.

Methods for typing DNA based on mass spectrometry can also be used. Such methods are disclosed in U.S. Pat. Nos. 6,613,509 and 6,503,710, and references found therein.

Polymorphisms in DNA sequences can be detected or typed by a variety of effective methods well known in the art including, but not limited to, those disclosed in U.S. Pat. Nos. 5,468,613, 5,217,863; 5,210,015; 5,876,930; 6,030,787; 6,004,744; 6,013,431; 5,595,890; 5,762,876; 5,945,283; 5,468,613; 6,090,558; 5,800,944; 5,616,464; 7,312,039; 7,238,476; 7,297,485; 7,282,355; 7,270,981 and 7,250,252 all of which are incorporated herein by reference in their entireties. However, the compositions and methods of the present invention can be used in conjunction with any polymorphism typing method to type polymorphisms in genomic DNA samples. These genomic DNA samples used include but are not limited to genomic DNA isolated directly from a plant, cloned genomic DNA, or amplified genomic DNA.

For instance, polymorphisms in DNA sequences can be detected by hybridization to allele-specific oligonucleotide (ASO) probes as disclosed in U.S. Pat. Nos. 5,468,613 and 5,217,863. U.S. Pat. No. 5,468,613 discloses allele specific oligonucleotide hybridizations where single or multiple nucleotide variations in nucleic acid sequence can be detected in nucleic acids by a process in which the sequence containing the nucleotide variation is amplified, spotted on a membrane and treated with a labeled sequence-specific oligonucleotide probe.

Target nucleic acid sequence can also be detected by probe ligation methods as disclosed in U.S. Pat. No. 5,800,944 where sequence of interest is amplified and hybridized to probes followed by ligation to detect a labeled part of the probe.

Microarrays can also be used for polymorphism detection, wherein oligonucleotide probe sets are assembled in an overlapping fashion to represent a single sequence such that a difference in the target sequence at one point would result in partial probe hybridization (Borevitz et al., Genome Res. 13:513-523 (2003); Cui et al., Bioinformatics 21:3852-3858 (2005). On any one microarray, it is expected there will be a plurality of target sequences, which may represent genes and/or noncoding regions wherein each target sequence is represented by a series of overlapping oligonucleotides, rather than by a single probe. This platform provides for high throughput screening a plurality of polymorphisms. A single-feature polymorphism (SFP) is a polymorphism detected by a single probe in an oligonucleotide array, wherein a feature is a probe in the array. Typing of target sequences by microarray-based methods is disclosed in U.S. Pat. Nos. 6,799,122; 6,913,879; and 6,996,476.

Target nucleic acid sequence can also be detected by probe linking methods as disclosed in U.S. Pat. No. 5,616,464, employing at least one pair of probes having sequences homologous to adjacent portions of the target nucleic acid sequence and having side chains which non-covalently bind to form a stem upon base pairing of the probes to the target nucleic acid sequence. At least one of the side chains has a photoactivatable group which can form a covalent cross-link with the other side chain member of the stem.

Other methods for detecting SNPs and Indels include single base extension (SBE) methods. Examples of SBE methods include, but are not limited, to those disclosed in U.S. Pat. Nos. 6,004,744; 6,013,431; 5,595,890; 5,762,876; and 5,945,283. SBE methods are based on extension of a nucleotide primer that is adjacent to a polymorphism to incorporate a detectable nucleotide residue upon extension of the primer. In certain embodiments, the SBE method uses three synthetic oligonucleotides. Two of the oligonucleotides serve as PCR primers and are complementary to sequence of the locus of genomic DNA which flanks a region containing the polymorphism to be assayed. Following amplification of the region of the genome containing the polymorphism, the PCR product is mixed with the third oligonucleotide (called an extension primer) which is designed to hybridize to the amplified DNA adjacent to the polymorphism in the presence of DNA polymerase and two differentially labeled dideoxynucleosidetriphosphates. If the polymorphism is present on the template, one of the labeled dideoxynucleosidetriphosphates can be added to the primer in a single base chain extension. The allele present is then inferred by determining which of the two differential labels was added to the extension primer. Homozygous samples will result in only one of the two labeled bases being incorporated and thus only one of the two labels will be detected. Heterozygous samples have both alleles present, and will thus direct incorporation of both labels (into different molecules of the extension primer) and thus both labels will be detected.

In another method for detecting polymorphisms, SNPs and Indels can be detected by methods disclosed in U.S. Pat. Nos. 5,210,015; 5,876,930; and 6,030,787 in which an oligonucleotide probe having a 5′ fluorescent reporter dye and a 3′ quencher dye covalently linked to the 5′ and 3′ ends of the probe. When the probe is intact, the proximity of the reporter dye to the quencher dye results in the suppression of the reporter dye fluorescence, e.g. by Forster-type energy transfer. During PCR forward and reverse primers hybridize to a specific sequence of the target DNA flanking a polymorphism while the hybridization probe hybridizes to polymorphism-containing sequence within the amplified PCR product. In the subsequent PCR cycle DNA polymerase with 5′→3′ exonuclease activity cleaves the probe and separates the reporter dye from the quencher dye resulting in increased fluorescence of the reporter.

In another embodiment, the locus or loci of interest can be directly sequenced using nucleic acid sequencing technologies. Methods for nucleic acid sequencing are known in the art and include technologies provided by 454 Life Sciences (Branford, Conn.), Agencourt Bioscience (Beverly, Mass.), Applied Biosystems (Foster City, Calif.), LI-COR Biosciences (Lincoln, Nebr.), NimbleGen Systems (Madison, Wis.), Illumina (San Diego, Calif.), and VisiGen Biotechnologies (Houston, Tex.). Such nucleic acid sequencing technologies comprise formats such as parallel bead arrays, sequencing by ligation, capillary electrophoresis, electronic microchips, “biochips,” microarrays, parallel microchips, and single-molecule arrays, as reviewed by R. F. Service Science 2006 311:1544-1546.

The markers to be used in the methods of the present invention should preferably be diagnostic of origin in order for inferences to be made about subsequent populations. Experience to date suggests that SNP markers may be ideal for mapping because the likelihood that a particular SNP allele is derived from independent origins in the extant populations of a particular species is very low. As such, SNP markers appear to be useful for tracking and assisting introgression of QTLs, particularly in the case of Genotypes.

EXAMPLES

The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Example 1 Identification of a Locus Associated with Yellow Flash

In yield trials being conducted at Thomasboro, Ill. in August, 2003, it was observed that some F3:5 soybean lines of the pedigree A3525/DKB31-51 (that contained a transgene that confers glyphosate tolerance and exhibited yellow flash when sprayed with glyphosate (i.e. ROUNDUP WEATHERMAX®) while other lines of the same pedigree showed glyphosate tolerance and no yellow flash symptoms. Repeat experiments conducted in 2004 produced similar results in 130 F3:6 lines in yield trials conducted at Hopedale, Ill. A3525 is a commercially available Asgrow® soybean variety and is also known under the variety name SN70025. DKB31-51 is described in U.S. Pat. No. 6,346,658 and samples of this seed have been deposited previously under ATCC accession number PTA-3871.

Fifty-three lines were categorized as either “Flash” or “No-Flash” with the remainder of the material falling between the extremes.

The fifty-three lines categorized in 2004 were planted at Covell, Ill. in 2005 and were sprayed with ROUNDUP WEATHERMAX® at a rates of about 42 oz/acre on a weekly basis beginning at about the V3 to V4 stage for up to four weeks, thus in certain instances attaining a total rate of glyphosate exposure of a 4 week span of about 168 oz/acre. Tissue samples were collected from one individual plant from each of fifteen lines that demonstrated the most severe yellow flash and fifteen that showed no symptoms. Table 4 shows the breeding and testing history of the materials used in this study.

TABLE 4 Breeding and testing history of the materials Gen. Season Year Location Bulk/SPS/Prow/PRYT Cross Summer 01 Ames, IA Cross F₁ Winter 01 Isabella, Puerto Rico Bulk F₂ Winter 01 Isabella, Puerto Rico Pod Pick F₃ Summer 02 Bloomington, IL SPS F₄ Winter 02 Rancagua, Chile Progeny Row F₅ Summer 03 Bloomington, IL Yield Trial F₆ Summer 04 Bloomington, IL Yield Trial F₇ Summer 05 Bloomington, IL Spray Trial SPS: Single Plant Selection. Prow: Progeny Row. PRYT: Progeny Row Yield Trial.

Example 2 Identification of Molecular Markers that are Associated with a “Yellow Flash” Phenotype

To identify marker associated with yellow flash symptom, we used a “Genome Scan” approach. Fifteen samples from lines showing no flash and 15 samples from lines with severe flash were collected from a segregating population (F3:6). DNA were extracted from these 30 samples and used as templates to screen a set of 2746 SNP markers that provide a high-density coverage of the entire soybean genome with approximate two markers per CentiMorgan Unit (cM). Allelic scores at each marker were collected and compared across 30 lines. Of the 2746 markers tested, 776 were segregating and 226 were heterozygous. Two markers, M0102027 and M0101742, clearly showed one allele in no flash and another allele in flash samples (Table 5), indicating a linkage between these two markers and the phenotypes. Having 15 plants showing the same allele and the same phenotype by chance is very low (½¹⁵). Therefore, this could not be explained by a random event. A third marker, M0129138, show one allele on the flash lines and another allele on 14 out of 15 no flash lines, indicating a linkage of this marker to the flash phenotypes. M0101742 and M0129138 turned out to be mapped on the same chromosomal location with no recombination on the mapping population. Other data supporting the linkage is that all seven commercial varieties with known flash phenotypes matched perfectly with the allelic data on the two markers.

TABLE 5 Genotypes for Yellow Flash Phenotype Map Posi- Flash Varieties No Flash Varieties Linkage tion DKB26- DKB31- DKB38- 037014- Locus Group (cM) 52 51 52 CI3478 AG3602 AG3305 11-18 A3525 M0101742 L 2.4 CC CC CC TT TT TT TT TT M0129138 L 2.4 AA AA AA GG GG GG GG GG M0093116 L 4.0 AA AA AA AA AA AA AA AA M0129925 L 4.0 CC CC CC CC CC CC CC CC Phenotype FL FL FL ? NF NF NF NF FL: exhibit yellow flash phenotype NF: exhibit a no flash phenotype

Example 3 Analysis of the Genotype of Soybean Varieties and Yellow Flash Phenotype

Approximately 1,700 soybean varieties (lines) were assayed or typed for the presence or absence of allelic variants of the markers M0101742 (SEQ ID NO: 5), M0129138 (SEQ ID NO: 4), M0093116 (SEQ ID NO: 6), and M0129925 (SEQ ID NO: 7). Of these lines, complete scores for all four markers were obtained in 844 lines. A summary of the genotypes observed in these 844 lines is provided in Table 6.

TABLE 6 # Samples (lines) Genotype¹ Phenotype 706 TTGGAACC No Flash 193 CCAAAACC Yellow Flash 113 CCAATTGG 46 TTAAAACC 43 TTGGAAGG 16 TTGGTTGG 11 TTAATTGG 9 CCAATTCC All Plant Introductions (PIs) 8 CCAAAAGG 5 TTGGTTCC 4 TTAATTCC All Plant Introductions (PIs) 3 TTAAAAGG All Plant Introductions (PIs) 1 CCGGTTGG All Plant Introductions (PIs) ¹The genotype of a line is shown as N1N2N3N4N5N6N7N8, where N can be A, T, G, or C depending on the position and the line and where N1 is nucleotide 1, N2 is nucleotide 2, N3 is nucleotide 3, N4 is nucleotide 4, N5 is nucleotide 5, N6 is nucleotide 6, N7 is nucleotide 7, and N8 is nucleotide 8. The genotype represents the both the paternal and maternal allelic forms of the markers M0101742 (SEQ ID NO: 5; position 1206; nucleotides 1 and 2 in genotype shown), M0129138 (SEQ ID NO: 4; position 218; nucleotides 3 and 4 in genotype shown), M0093116 (SEQ ID NO: 6; position 183; nucleotides 5 and 6 in genotype shown), and M0129925 (SEQ ID NO: 7; position 328; nucleotides 3 and 4 in genotype shown). Thus the genotype “TTGGAACC” means that the line is “TT” for both the paternal and maternal contributions to the M0101742 polymorphism, “GG” for both the paternal and maternal contributions to the M0129138 polymorphism, “AA” for both the paternal and maternal contributions to the M0129116 polymorphism, and “CC” for both the paternal and maternal contributions to the M0129925 polymorphism.

Sixty 63 soybean varieties were subsequently selected from various genotype groups and tested for yellow flash essentially as described in Example 1 (i.e. were sprayed with Roundup WeatherMax® at a rates of about 42 oz/acre on a weekly basis beginning at about the V3 to V4 stage for up to four weeks, thus in certain instances attaining a total rate of glyphosate exposure of a 4 week span of about 168 oz/acre). The results of those analyses are provided in Table 7.

TABLE 7 Genotypes and Phenotypes of Selected Varieties M0101742 M0129138 M0093116 M0129925 Overall (SEQ ID (SEQ ID (SEQ ID (SEQ ID Flash Number of NO: 5)¹ NO: 4)¹ NO: 6)¹ NO: 7)¹ Score² Phenotype lines tested CC AA TT GG 1.8 No flash 14 CC AA AA CC 4.4 Flash 15 TT GG TT GG 2.4 Partial resistance 1 TT GG AA GG 2.6 Partial resistance 3 TT GG AA CC 1.7 No Flash 30 The genotype represents the both the paternal and maternal allelic forms of the markers M0101742 (SEQ ID NO: 5 position 1206), M0129138 (SEQ ID NO: 4, position 218), M0093116 (SEQ ID NO: 6; position 183), and M0129925 (SEQ ID NO: 7, position 328). Flash Rating Scale: 1: Green-No Yellowing 2: Mostly green, very slight yellowing <5% (1-2 plants with some yellowing) 3: 5-10% plants with yellowing 4: 11-20% plants with yellowing 5: 21-35% plants with yellowing 6: 36-50% plants with yellowing 7: 51-65% plants with yellowing 8: 66-80% plants with yellowing, some necrosis 9: 81-100% plants with yellowing and or necrosis

For optimal prediction of yellow flash phenotype, all four markers (M0101742, M0129138, M0093116, and M0129925) can be used. However, one can achieve high predictability with only two markers, M0101742 and M0129925. Based on fingerprint information, these two markers would identify two genotypes: CCAAAACC and CCAATTCC. CCAAAACC is the predicted genotype for plants which exhibit yellow flash (193/844 varieties screened based on fingerprint analysis). CCAATTCC is an additional genotype which only represented 9/844 varieties based on fingerprint data. All 9 varieties comprising the CCAATTCC genotype were Plant Introductions (PIs). As used herein in reference to soybean, Plant Introductions (PIs) refer to mostly typical germplasms that have not been subjects of breeding improvements. For example, PIs are include lines that have not been obtained by intercrossing followed by selection. PIs can also include lines obtained from seeds or vegetative propagules of plants that have been introduced from another country. Therefore, the two markers M0101742 and M0129925 could distinguish between the three most common genotypes observed: CCAAAACC (associated with a yellow flash phenotype), TTGGAACC (associated with a non-flash phenotype) and CCAATTGG (associated with a non-flash phenotype). More specifically, where M0101742 is CC and M0129925 is CC, one would predict that most soybean lines thus identified, and that were obtained from, or related to, the varieties analyzed in this Example, would have a Yellow Flash phenotype.

Example 4 Genotypes and Phenotypes of Various Commercial Varietie

In field tests conducted in 2006, a number of commercial varieties were genotyped with the markers M0101742 (SEQ ID NO: 5), M0129138 (SEQ ID NO: 4), M0093116 (SEQ ID NO: 6), and M0129925 (SEQ ID NO: 7) and exposed to glyphosate to test for the presence or absence of the yellow flash phenotype essentially as described in Example 1 (i.e. were sprayed with ROUNDUP WEATHERMAX® at a rates of about 42 oz/acre on a weekly basis beginning at about the V3 to V4 stage for up to four weeks, thus in certain instances attaining a total rate of glyphosate exposure of a 4 week span of about 168 oz/acre). The results of this analysis is provided in Table 8.

TABLE 8 ATCC M0101742 M0129138 M0093116 M0129925 Depository Branded (SEQ ID (SEQ ID (SEQ ID (SEQ ID U.S. Pat. Variety Name Accession Name¹ NO: 5)¹ NO: 4)¹ NO: 6)¹ NO: 7)¹ Phenotype No. in Patent Number² AG4201 CC AA AA CC Flash 7,071,388 SE71112 PTA-5728 AG4601 CC AA AA CC Flash 5,659,116 927113675 97556 AG4603 CC AA AA CC Flash 7,067,723 SE73753 PTA-5730 AG4702 CC AA AA CC Flash 5,750,857 9390369478967 209547 AG4902 CC AA AA CC Flash 6,143,953 931474956907 PTA-2214 DKB31-51 CC AA AA CC Flash 6,346,658 950045734453 PTA-3871 DKB37-51 CC AA AA CC Flash 7,294,764 SD82997 PTA-5737 DKB38-52 CC AA AA CC Flash 6,660,912 SD92955 PTA-5382 DKB40-51 CC AA AA CC Flash 6,683,233 SD93038 PTA-5329 DKB46-51 CC AA AA CC Flash 6,933,423 SE73090 PTA-5733 AG0801 TT GG AA CC Non-Flash 6,005,170 9422009600716 PTA-269 AG0803 TT GG AA C Non-Flash 7,498,489 4498438 PTA-9064 AG0901 C A T G Non-Flash 6,080,917 942193611352 203207 AG2403 T G A G Non-Flash 6,900,372 SN71173 PTA-5727 AG2603 T G A C Non-Flash 7,388,131 4599695 PTA-9070 AG2703 T G A C Non-Flash 6,184,442 9323265446452 PTA-2577 AG3006 T G A C Non-Flash 7,482,516 0387907 PTA-9029 AG3302 T G A C Non-Flash 5,973,235 943470629664 203939 AG3505 T G A C Non-Flash 7,569,750 4559809 PTA-9023 AG3703 T G A C Non-Flash 6,881,879 SW90702 PTA-5738 AG3903 T G AA CC Non-Flash 6,632,982 SW84112 PTA-5299 AG4403 T G A C Non-Flash 6,348,644 9472569612611 PTA-3870 AG4503 T G A C Non-Flash 7,378,578 0358232 PTA-9003 AG4703 T G A C Non-Flash 7,554,014 437973 PTA-9066 DKB06-51 C A T G Non-Flash 6,143,953 931474956907 PTA-2214 DKB08-51 T G A C Non-Flash 7,504,565 4878185 PTA-9702 DKB22-52 T G A C Non-Flash 6,858,783 0491727 PTA-6187 DKB29-51 C A T G Non-Flash 6,884,927 0509249 PTA-6272 DKB42-51 T G A C Non-Flash 7,479,582 4671685 PTA-9027 ¹The genotype represents the both the paternal and maternal allelic forms of the markers M0101742 (SEQ ID NO: 5 position 1206), M0129138 (SEQ ID NO: 4; position 218), M0093116 (SEQ ID NO: 6; position 183), and M0129925 (SEQ ID NO: 7; position 328) ²Deposit numbers of seed available through the American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, Va., USA, 20110-2209.

Example 5 Exemplary Marker Assays for Detecting Polymorphisms

In one embodiment, the detection of polymorphic sites in a sample of DNA, RNA, or cDNA may be facilitated through the use of nucleic acid amplification methods. Such methods specifically increase the concentration of polynucleotides that span the polymorphic site, or include that site and sequences located either distal or proximal to it. Such amplified molecules can be readily detected by gel electrophoresis, fluorescence detection methods, or other means. Exemplary primers and probes for amplifying and detecting genomic regions associated with a no flash phenotype are given in Table 9.

TABLE 9 Exemplary Assays for Detecting Polymorphisms Marker or SEQ ID SEQ ID Locus Marker SNP Forward Reverse SEQ ID SEQ ID Name SEQ ID Position Primer Primer Probe 1 Probe 2 M0129138 4 218 17 18 19 20 M0101742 5 1206 21 22 23 24 M0093116 6 183 25 26 27 28 M0129925 7 328 29 30 31 32

Example 6 Oligonucleotide Probes Useful for Detecting Polymorphisms by Single Base Extension Methods

Oligonucleotides can also be used to detect or type the polymorphisms disclosed herein by single base extension (SBE)-based SNP detection methods. Exemplary oligonucleotides for use in SBE-based SNP detection are provided in Table 10. SBE methods are based on extension of a nucleotide primer that is hybridized to sequences adjacent to a polymorphism to incorporate a detectable nucleotide residue upon extension of the primer. It is also anticipated that the SBE method can use three synthetic oligonucleotides. Two of the oligonucleotides serve as PCR primers and are complementary to the sequence of the locus which flanks a region containing the polymorphism to be assayed. Exemplary PCR primers that can be used to type polymorphisms disclosed in this invention are provided in Table 4 in the columns labeled “Forward Primer SEQ ID” and “Reverse Primer SEQ ID”. Following amplification of the region containing the polymorphism, the PCR product is hybridized with an extension primer which anneals to the amplified DNA adjacent to the polymorphism. DNA polymerase and two differentially labeled dideoxynucleoside triphosphates are then provided. If the polymorphism is present on the template, one of the labeled dideoxynucleoside triphosphates can be added to the primer in a single base chain extension. The allele present is then inferred by determining which of the two differential labels was added to the extension primer. Homozygous samples will result in only one of the two labeled bases being incorporated and thus only one of the two labels will be detected. Heterozygous samples have both alleles present, and will thus direct incorporation of both labels (into different molecules of the extension primer) and thus both labels will be detected. Exemplary forward and reverse SBE probes are provided in Table 10.

TABLE 10 Exemplary SBE Probes for Detecting Polymorphisms Marker Probe or Marker (SEQ Locus SEQ ID SNP ID Name NO: Position Probe (SBE) NO.) M0129138 4 218 TGTGTCCTATATGATCTT 19 M0129138 4 218 TGTCCTGTATGATCTTA 20 M0101742 5 1206 TGACTAGCATGTATCTAT 23 M0101742 5 1206 ATGACTAACATGTATCTAT 24 M0093116 6 183 CCAACACCAAACTA 27 M0093116 6 183 CAACACCAAACAAA 28 M0129925 7 328 AGTAGTAGCTAGTGAAATA 31 M0129925 7 328 AGCTAGTCAAATATTT 32

Example 7 Summary Table of Nucleic Acid Sequences

TABLE 11 Nucleotide Sequences Marker or SEQ Locus ID Name NO: Sequence M0205350 1 gggcttctccgctcgaacttatgcaagggctatgtgatggtgatgatgattgaatttgaagctgctactgca ttactctctttggtaatgaatttgaagaagcagaaagaaaggaaatgatggtctttacaccgtcaattttaat atwtgtaagtgtaaactctgtagtagcacagtgatgtagtgtagattaggcatttggcagcgtggtaaatat tcttagattgaattgtgttatcaacagtattaaacgttttaggctgaatgaatgatattgatgaatttataaggt ggggaggctaagatggaatcatgtagtta M0114388 2 aattacacacatcatgatcttgtaatcatcatctcccaaatcagggatagccttggccttcttacc ccagggattccataccactgcactctcattatcaccaaaccaataagtgacatcaattgtagattaaattaa caaacttatgtaaatctgaatgctggatctggcccttataaagtgaaaaacacgttgtagagactaaagta agtaatccccttgtttttgatgaggaaatgaacagttgatattatgtgcacttgtataacaaaacatggatatt ttaaaatatcagtcgttgattttctcatcaataaattaggattgttttactctctaaagtgacttgttcagattaga agagccaaatagatacaatgccatgcaaaatttttattctctgactaataactaataacaacctgcatctgg cattcctttcttctggagtacaaaagttctttttttctcatggtctatgatggcaattttagttgggctrtgcaagt acactctgtccatctacaaggtaaccacaaatgtccttagagaacacttgaaaaaaaagttgatttggtatc tattatatatattcatacactcgaaaatcaatcagaatatatataggttatgtgcacttatgtgcttatgatgtca attttcttagcctgtgagacacctccaaccaattgaatgaaaggaccagaaaatcaaattatacctctccat caaaagtgagtgcatctgcctgctctgtgaaccttgatctgttcaacagattgtcaaagtaatccagtgtct ccaatccctcaatacgcacttc M0205928 3 attcctatttcctacacaacactacactgtctggtggaagaatctcttcactctccatgcaacaacgttggct atgtctccttattctctctctttgttagcctctgtctcccccaaaatgcacacccttctttctttctcctcatcaca ctctccacatcttccaaaccacaacataaccaaatccaataataaactctctcattccatcaatggactttca tcmtgcccttcttctcctttgctccccagtgccacaaaatcttctccctttctcatttccacttcaaaaattgca tctttcagggtccttgctgcttcctctatacctgatgctagaagtgatgaaccagccaaaactagtgatttctt aaaaactcttcag M0129138 4 cgccagcttgcatgcctgcagttccaagaattatttcaaaccgctgcttccattttagaatccttgttatgtcc ttttctgcacagtagattagtatgtcacaagttgcatgttgggccggttgattttatgaaattaataagagtta aatatgtttttagtccttgcaaataggaaaaagttctccttttggtcctcaattatgaaaatgtgtcctrtatgat cttatttacataaatgaggaaatgaaagcagatgatacttttatgaaggacaaagattacatttgacacatttt cataaatgagtgactaaaaagaagcattttattttttagtgattaaattaattggaaacattacaagattactttt ggtcatgggttcaagaatccggaaacagtttctttgcatatgcaagggtaatgctgcttacaatatccctcc cccataccttggcatagtgaggagcctccgggcaatggaatacactagtttttatagtacaatatttttcattt agagttactgtgggacaaaaggaacttaccaaaaatgaattgatctaagctcttgttaggtaggtactcata cacaatgaggctctcagggccttcaatgctgcaacccaatagtttgacaaggttcttgtgttgcattccact aatcaaattcacttcattgaagaaatcatccacccattgcctattattgaagaccaatctcttaacagcaaca tcattcccatttggcagagtccctttgtatacagaaccagatcctccttgacctatctttcttgaagagctgaa ataatccgtcgccttctctagagtttcatatttgtaattcaagctagaattcttcaaggaaggaggaacctca ataaaattgttttctgagtgattcaggagaaaatgaaatacagcatcagcaaaattaacaaacaatcattcc aaatatatattattggtatgaacaagagtgttctccagaacattacttcttctctttttggtgaaggccacataa gagactgcaagagtgagaactacaac M0101742 5 acacagaaatcacaaacaagtggtgactacttacccatattcaccaaagaaatggaaaaacttctagaac ttgtgacaaaacaaaactgggggactcactctgagggcatgtcatcaacaacaaccactcctatctatgg cttggcacaatgcttccaagacctttccagcattgattgccttcaatgctttgcagccagccgcaccaagct ccctcgctgcctcccttcggtttcggctcgaatttaccttgatggctgcttccttcgctatgacaattacagtt tctacactgaaaactatgaccctttgagggacacagtgaattgcacctcagagtatggttctgtggttggtg atggtgagaagttggtgtttgctgagagtgttggcaaagtggttgagagtgtggtgagggtggctgtgaa taataatgagggaagaggcttttttgcagttggagaaggtgggggagtttatgcattggcacagtgctgg aaaactgttggggtaaaagggtgtagtgattgcttgaggaaagctgaaaatgaggtcaaaggatgtttgc ctaagagggaagggagggccttgaatactgggtgctatttgagatactcaactgttaagttctacaatcaa ggaggtcaagatggtcaaggagatggtaagagctgttgctctagtttgaagtttttatattcttcattagtttc ttggttccttttggataaacttctcaaccactagttataggagaaaaaaatgaattaaacatctcttgtaagtt aaaatcaatttgtgcacttcgataagttttataaaaactctctcgtttaacttttccaaaagctgagatgtataa gttaattttaacttacagaagaagtttgattcatttttgctttttatgttcttctcctttaagtatttattgagaagc ttatcggttggaatttggaaactgaagctcaactgggaatttcaattgcatattgttaccatgcagtttcaaattc cttgtgttgcttataggttaaatgacaaatggagaaggaaagaagtaaagatgaatgttactgtatcattgt gaatgaaatgctgcttttcaactttaactttgctataactcttaggttagttttggtgtctaaagtttgtcctgaat agaatcctaggtttcagttcatagatggcatagatacatgytagtcatttattttgtatacatgttgatgcaatt gtccatgttttaatttttcagattcttccagaaaacgagtcattatagcagcagggtcagtctt M0093116 6 attatatgagggctcttgggtttttcaaggacactgatgcacccttacctgtaagaatatgattttgttattatt attattatatttattgtgagtctatatatataagaagaattttccattttgtttcatctaattaatatagttttaata atttttaaattttgctttgtttaatgcttwgtttggtgttggaaattaagattgttccagggtttgatgctgctggtg tggtggtgagagtgggaagtaaagtgagcaaattcaaggttggagatgaagtttatggtgatatcattgag tatgcttggaataatccaaagaccattgggactttggcagaatatactgctactgaggagaaagtgttggc tcacaaaccctccaatttaagctttattgaagcagctagcctt M0129925 7 aggcaccaaaccaagggatttaaaatttattaaattataaacatgaaatgattaaataaagagttgaattcc cataattttatacgttttattaaatttcactcagcaaaaaatgtattaaaaaatatattattcccatttgtctgtctt tatttatgtcatctattttaatttttctgatgtatttaactggggccaaactgaaacatgttgatcatgcaaaggc ctactcaccatttcacatgtacgtgtcatcacccagcaaccccatttttctacataacacacactccctctct aacactcacactccaataacaaatatttsactagctactactcttcttagtttctctgttgtatcatttttattgcta tatcctaatcaaacttcactctcaaaatgagtgatcccacactagcacaacagcatctagtcaaagtccac acaacaacacacgaaacagttgttaccacacacaatcataaccaaacaccctcaataaatgtgtgttact gaattatttaattatttgtacacctaactatgattaatatttaattcttcaaaactttgtttatgcatgataaccgtg attaatttttatttttttcccctatgattgagaacaggcctcaggtgaaaagaagaagattgtgggggtgttct acaaagggaatgaatatgctaaattgaatccaaattttgttggatgtgttgaaggtgcattgggaatacgtg agtggctggaatcacagggtcatcagtacattgtcactgatgacaaagaaggacctgattctggttagta cttagtatcttgccaacttaattcaagtttgagtaaactattattttgatgatttgatctataaaagtgtacaaca ttgtgaaattagtctctaacattgtcacattagtctctgaaattaagataatttcatatgacaaatgacatgttat taactctttttcgtactgtaaattgaaaaatgtggctacgtgttatatgaaaattggttgggacctggtctcgg atcatgtaataatttctatcaaacaaggtatcagagtaatcaacactataatatcatggaatgcaaatgtgttt gtcccttcaagattttaattgcttgaactcaatggaatttgatgttct M0205537 8 aggaaatactagattttgatatactattatttaataattttcctactcgactaaaatgaaaaaaaaaacactaa aataatgatatcactaatattattagctgaattttttttgtttgttgaatctttagttgactgaatttagtatttgac taaaamaagaatcatatcacaaactaatttgcctgtaactcattgctttaatttgcttttaataattgtcagcaa gtctagatttttaatgattagatagatagctaacaaaaataccacactggatacatatgaaatcaatattaag tttaaagagatgcaatacgcaatcgatttgattaatgaatttcaaatgttctgcgttaatttattcaattacctttt aaattgaatgttttcattcctgggctctg M0202715 9 atgatgggatcttgcatatgcccgttggagactccggcgaggttgctttggaccacaagcttcttccgtca taagcttatgatcttctaataattaataattcacgcacacaaacaaacaaacaaacaaacaaaaaacacttc ataacaacaacaacaacccttctgaaattctcaacacaagtttcaaaaaacagagtaaaagaaacagag caaaaacacacacacaaaaacacaaacacagacaccttttaagtattaaggtgtctctttctctcsccgga aagtttctccgtcggcggtggtgattgaccggagtgccatggagtctggacggattttctttggtgcctctg cttcaagcggcaacaacatgctctttctcggcacaactgaact M0206286 10 tagtaaagccaccaactccaacaccaacttccccagtggtgtaccctcctcctnnntttccatctccacca gctcctgtagtgaaatcaaacaagggtaagtgtgtaccacatctatstctttagtaactcctttccgatctcta atgtaattaaatgaaatgattctgtcacatttttctgctaatttaacttttacgttatttagaaaaaaaatataaaa gaaatttgtatcactttttctttaaaaataggaaaaatatgtgtgataaaatagataatgttttacaatttcattac agaaatactttatattttataatgttaatattttttatttttcacaatttttttcttctttcttattagtttttggac ttaaattaaataatatttttaatcctgtcatgtgggttttagtattcttaatattattttcttgatttgattactgta aaatgttttagtaaggcttaactaaaacagacaaagaaaaatatttcaagaagattaaaatggaaaaaaagaatctta taatacatggattaaaaaattagtgaagccttacttttgtttttcttttctctttgttacacgtcttcaccttgttgt ctttgttatcctttttcacatctaatgatggatgtgagagaagaaccatgcatggtcttaattgtttatgtgattaat ggctttaaagtatagaacttttaagtaagatcagttgagttaattaatgaaacatggtcttttgttttccaaattt ttttgtgggcagattgcattccactaagggattataggtgctcattacactcaaggaagaaattgt M0206054 11 atcttggttttccaatcgcgcagcccgagcggccatcwgaacaacagtatctacgtcaactcctttagcaaaaatct acagaaaacattgaaaacacttgtgtgagcatacgacaaggcaaataagaaaacaacacagtacaaaactgacta cttctaacctcaataagattcttgtcaactgtcagtttattcaaagtcaaagttccagttttgtcgctacataataca tccattcctgccatctcttctattgctgtcattcttttagtaatagcaccctgcaatgattatataaagcataaacta taaagactaacatctaattgattaaaacttgagacaactgcttttcaagaagcactaatgtctacctgctgagctaag cgatgggatccaattgccattgtcactgacaaaacagtaggcatggcaataggaattcctccgataagaagcacgagc agattgtcaatcccaggacgatattcccggtgttgaattgggtacatgacaatgat M0205375 12 ctttgattcttgccagtctttttcattctttttcattcttaaatccatcaaatgaacctattgatatgactgaaacct ttggattagccaagactaaagctactccacttgagattttaattaagccacgattatcttctagttgttatytataaa agcatgtgaatcttgtcttagcggtttgtggaaagtctgttgttaaactatgtgatcttcttttagataaatcaggtt tgcctgataaattatattttcgtcaaaagggcatttttggaattcacaaaattgtcatcatgtggtgttgaaataagg tgtgttgtaataaggtttaaggctt BG406195 13 tattgtcttttgtgaatgatcaataacttcctaatggtaattcctttcattagagagcccatggatttatattcccat ggtttggaaaaaagttcttcaagcagtgtaagtaacaccaatggttttactgaaaatctggtattcggtgacgcttat taacatcaatttgaccaatggttttactatggacgcttattaacatcagttaacggtatgaagcttgggaaagctgtt ggaaaatggggtctttgagatgcttgatgcaagtttgccatcatgacttccatttcacacttagacattgagtggtga acgtccatagtatttgatataaatg BU082700 14 gcaccagtccacacaaagaagattgtccacagagatgttaaaacagaaaatatgcttctggacaagacacgaacc ttgaaaatagctgattttggagtagctcgtattgaggcctccaatcctcatgacatgacaggtgaaactggaaccctt ggttacatggctcctgaggtacatgcttcaattcctttgaaaatttctctctcctgtgcattgttcttttggggtttg tttcaaacacccttaatgtctagtccttacctcagaaaattttgaaaatgctggcttaggacttgttacttgcgaccg gctctgttgtctaactaattgtgaaagaactgggttgaatatttttggacttaaaatataaggaaaaattactaaaca ggaattcttgattaaaatattaaccatgttggaaagataaggacattgaattgttccatcactgtccttactttcatc aggaattccttttgttttatagttcacccaacaattatgtatatatccatgttggttttggtacataattacaggaag aaatctttacctcagtcccatttacaattactgagatctagaactgcagcatgtcactactcactaatcttga TA14086_(—) 15 atggcaagcatttctagcattccatcacacataaaaacttgggtttattctgaatatgggaacacagaagagattcta 34305 aaatttgatcccaacgtacctataccagacatcaaggaagaccaggtgctcatcaaggttgtggctacagctcttaat cctgtggattataagagggctcttggctatttcaagaacactgactctcccttacctgtaagatcatgattttaaatt tatatttgcgtggattattaattagtatagtttccattttgtataccaccttatataattcttttttgtttaaatata tttttagtttttataatttatatttttttgttttttgttattgtaaaattatttttttgtttttgtttttataaatta tgtttgttttatttttctttcctaaattattttagataatgttttgaatagtaaaaaaatattataacaataaaaaat aaaataaacataatttgtaagaatcaaaaataaaaaataatttgtaagtaaaaaaataaaaaataaataaattataag gattaaaattgtatttaagccatttttttttatcattgcattgtttaatttgtgtttggtttttgaaattaagagtgt tccggggtacgatgttgctggtgtggtggtaagagtgggaagtaaagtgaggaaattcaaggttggggatgaggttta tggtgatatcaatgagtatgctgtgaataatccaaagaccattgggactttggcagagtacactgctactgaagagaa attgttggctcacaaaccctccaatttgagctttattgaagctgctagccttcctttagctatcatcactgcttatca aggacttgaaagagttgatttttctgctggaaaatctatacttgttctaggaggtgctggtggagttggatcccttgt tattcaggtttgatatcttccatctccattggttaatttgacaataagtttcaattaaacagtgtcttactgaaatat tgagccattaatttcactttttcagtattttagttatttattttattcttcttctctaatcatatgatttaggagcaa tgatatttagatatctctctaaatttcagacacctcatatcatatcatttatcatttatttatattttctctttcctc tctatctctcttagcataattatataattaataatgaattgttgggtatttgattgatatgatgtagctcg ccaagcacgtttttggcgcatccaaggttgcagctactgctagttccgcaaaactggatttattaaggaacttggga gcagactttcctattgattacacaaaggagaattttgaagagcttgcagagaagtttgatgtagtgtacgatacaata ggtcagatgttgaaattgaacttaaattatttgtttcacatgaagtcagtttggtcatgactaatacaatattaacat atgagatgtggtatgagtacaacaattggtacagaactattagtttttatacctatcttacttatttatgacatgtaa taaataatgtacaccagagatattaacacaaaagaatgttgttatacaattaatttaaagtgcattaacatgtaacat acaacttattacttttgttatcttattattgattaccatgtgtaataagattgttgataataataaattactttaaga attgttatctattttttttattagtggatagtataaaagtattttcatgtgtatcaatattattattgaaaatgaaga catggttgattccaaaaacagggcagagtgacaaggcattgaaggctatcaaagaaggggggaaagttgtgacaatag caccaccagcaactccacctgctatcccattctttctcacttcagatggtgctgtgttggagaagttacaacctcact tagaaagtgggaaggtgaagccagtattggatcctaagagtccctttccattttctcagattgtggaagcatattcat acttgaagacaaatagagccattgggaaagtagtcatacatcccatcccttgaacatatataactatgcaaatatact atcaagtcctgctgtgcattctgaccttaatttgtgttaataaggttaatatttatatgattgataaggagagagc BU551345 16 tttagtcattagaattttacttgtttactcggttcgaaagttccatctcgctggtctcaattactattaaaaaatctc atattgcttacctcaattagtgggatgaggtttaagtacgtgatgaacaacttcacttnntgctaattagtttgaagt tataatgtaacatgctctatccttctttttggttggttgcttggggggagctcccnnnnacatggaattattgggaat caagcttccataattgtttcttcacttcttgatggcctaattaagctgcatgtgctagagaactcagaggggctgtag gacacaccaatcttcttaaatgtgtttgatgaggagctgtctatgctaaaacctaatggagatgtttgatct

Polymorphic nucleotide bases are designated in Table 11 and in the sequence listing provided herewith according to the WIPO Standard ST.25 (1998), Table 1, as follows: r=g or a (purine); y=t/u or c (pyrimidine); m=a or c; (amino); k=g or t/u (keto); s=g or c (strong interactions 3H-bonds); w=a or t/u (weak interactions 2H-bonds); b=g or c or t/u (not a); d=a or g or t/u (not c); h=a or c or t/u (not g); v=a or g or c (not t, not u); and n=a or g or c or t/u (unknown, or other; any.)

Having illustrated and described the principles of the present invention, it should be apparent to persons skilled in the art that the invention can be modified in arrangement and detail without departing from such principles.

Although the materials and methods of this invention have been described in terms of various embodiments and illustrative examples, it will be apparent to those of skill in the art that variations can be applied to the materials and methods described herein without departing from the concept, spirit and scope of the invention. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

Table 2 of the Specification Locus/ Display Name Start End ADDITTIONAL LOCUS (1) Source (2) Base (3) Base (4) INFORMATION (5) asmbl_11856 Vigna_unguiculata 16426 16586 NA TA2790_3886 Phaseolus_coccineus_release_2 16423 17393 ADP-ribosylation factor [Vigna unguiculata (Cowpea)] TA43459_3847 Glycine_max_release_2 16434 18055 ADP-ribosylation factor 1 [Oryza sativa (Rice)] TC276541 GMGI.071508 16434 18076 UniRef100_P36397 Cluster: ADP-ribosylation factor 1; n = 1; Arabidopsis thaliana|Rep: ADP- ribosylation factor 1 - Arabidopsis thaliana (Mouse- ear cress) = partial (38%) CD392203 Glycine_max_release_2 16216 18687 ADP-ribosylation factor [Glycine max (Soybean)] BQ610865 Glycine_max_release_2 16327 18667 ADP-ribosylation factor 1 [Oryza sativa (Rice)] EH046324 Arachis_stenosperma_release_5 16405 18745 Cluster: ADP-ribosylation factor 1, n = 1, Arabidopsis thaliana|Rep: ADP-ribosylation factor 1 - Arabidopsis thaliana (Mouse-ear cress) AW202311 Glycine_max_release_2 16378 19070 ADP-ribosylation factor [Glycine max (Soybean)] TC242702 GMGI.071508 16234 20195 UniRef100_Q38JU3 Cluster: ADP ribosylation factor 002; n = 2; core eudicotyledons|Rep: ADP ribosylation factor 002 - Daucus carota (Carrot) = complete BI321678 Glycine_max_release_2 17384 19066 ADP-ribosylation factor [Zea mays (Maize)] AW348317 Glycine_max_release_2 16355 20097 ADP-ribosylation factor [Glycine max (Soybean)] EH042959 Arachis_stenosperma_release_5 16401 20182 Cluster: ADP-ribosylation factor 1, n = 2, Medicago|Rep: ADP-ribosylation factor 1 - Medicago truncatula (Barrel medic) TC20337 LJGI.070108 16420 20191 UniRef100_Q5QQ33 Cluster: ADP-ribosylation factor 1, n = 2, Medicago|Rep: ADP- ribosylation factor 1 - Medicago truncatula (Barrel medic), complete EH047563 Arachis_stenosperma_release_5 16430 20182 Cluster: ADP-ribosylation factor 1, n = 2, Medicago|Rep: ADP-ribosylation factor 1 - Medicago truncatula (Barrel medic) TA2789_3886 Phaseolus_coccineus_release_2 16436 20196 ADP-ribosylation factor 1-like protein [Solanum tuberosum (Potato)] TA43462_3847 Glycine_max_release_2 16229 20438 ADP-ribosylation factor [Medicago sativa (Alfalfa)] TA1120_34305 Lotus_japonicus_release_1 16522 20191 ADP-ribosylation factor [Medicago sativa (Alfalfa)] TA2306_3848 Glycine_soja_release_2 16442 20440 ADP-ribosylation factor [Medicago sativa (Alfalfa)] TC273941 GMGI.071508 16426 20464 homologue to UniRef100_Q38JU3 Cluster: ADP ribosylation factor 002; n = 2; core eudicotyledons|Rep: ADP ribosylation factor 002 - Daucus carota (Carrot) = complete TC238119 GMGI.071508 16455 20449 UniRef100_Q38JU3 Cluster: ADP ribosylation factor 002; n = 2; core eudicotyledons|Rep: ADP ribosylation factor 002 - Daucus carota (Carrot) = complete EG373880 Arachis_hypogaea_release_5 17101 20182 Cluster: ADP-ribosylation factor 1, n = 2, Medicago|Rep: ADP-ribosylation factor 1 - Medicago truncatula (Barrel medic) BF066818 Glycine_max_release_2 17081 20378 ADP-ribosylation factor 1 [Populus tomentosa] BF596154 Glycine_max_release_2 17083 20397 ADP-ribosylation factor [Hyacinthus orientalis (Common hyacinth)] AW760997 Glycine_max_release_2 17116 20397 ADP-ribosylation factor [Hyacinthus orientalis (Common hyacinth)] BF424079 Glycine_max_release_2 17112 20417 ADP-ribosylation factor [Hyacinthus orientalis (Common hyacinth)] AW596022 Glycine_max_release_2 17121 20415 ADP-ribosylation factor 1 [Populus tomentosa] TA43446_3847 Glycine_max_release_2 17106 20436 ADP-ribosylation factor [Hyacinthus orientalis (Common hyacinth)] TA43455_3847 Glycine_max_release_2 17125 20452 ADP-ribosylation factor [Hyacinthus orientalis (Common hyacinth)] BW595867 Lotus_japonicus_release_1 17418 20191 ADP-ribosylation factor [Hyacinthus orientalis (Common hyacinth)] AW507598 Glycine_max_release_2 17343 20437 ADP-ribosylation factor [Hyacinthus orientalis (Common hyacinth)] TA43447_3847 Glycine_max_release_2 17343 20445 ADP-ribosylation factor [Hyacinthus orientalis (Common hyacinth)] TA43448_3847 Glycine_max_release_2 17355 20438 ADP-ribosylation factor 1 [Populus tomentosa] AW596189 Glycine_max_release_2 17358 20442 ADP-ribosylation factor 1 [Populus tomentosa] BI469983 Glycine_max_release_2 17410 20438 ADP-ribosylation factor 1 [Populus tomentosa] AW472058 Glycine_max_release_2 18655 20160 ADP-ribosylation factor 1 [Daucus carota (Carrot)] CB063805 Glycine_max_release_2 18623 20432 ADP-ribosylation factor 1 [Populus tomentosa] BM891090 GMGI.071508 18995 20429 homologue to UniRef100_A7PRL9 Cluster: Chromosome chr14 scaffold_27 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_27 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (42%) BM731935 Glycine_max_release_2 19949 20444 ADP-ribosylation factor 1 [Populus tomentosa] AW695591 MTGI.071708 30054 31388 similar to UniRef100_Q40542 Cluster: NPK2, n = 1, Nicotiana tabacum|Rep: NPK2 - Nicotiana tabacum (Common tobacco), partial (35%) TC130040 MTGI.071708 30054 31482 similar to UniRef100_A7PM42 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (30%) TC122822 MTGI.071708 30054 34162 Protein kinase, Nuclear transport factor 2 Pvcon9203 Phaseolus_vulgaris 31194 34247 UniRef100_A7PM42 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PM42_VITVI E-0 TA66103_3847 Glycine_max_release_2 31879 34559 Protein kinase; Nuclear transport factor 2 [Medicago truncatula (Barrel medic)] CA801261 GMGI.071508 33896 34304 similar to UniRef100_Q40542 Cluster: NPK2; n = 1; Nicotiana tabacum|Rep: NPK2 - Nicotiana tabacum (Common tobacco) = partial (16%) TC120073 MTGI.071708 35367 38178 Glycoside hydrolase, family 28 NP004759 GMGI.071508 34976 39622 GB|AF128266.1|AAD46483.1 polygalacturonase PG1 AF128266 Glycine_max_release_2 34980 39622 Polygalacturonase PG1 [Glycine max (Soybean)] TA69799_3847 Glycine_max_release_2 58988 65870 Ubiquitin-associated [Medicago truncatula (Barrel medic)] TA7619_47247 Lotus_corniculatus_release_1 63855 65940 Putative DNA cytosine methyltransferase Zmet3 related cluster TA8711_34305 Lotus_japonicus_release_1 63855 65940 UBA-like [Medicago truncatula (Barrel medic)] TC34762 LJGI.070108 65619 65940 NA Pvcon5587 Phaseolus_vulgaris 65216 67090 UniRef100_A7PM76 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PM76_VITVI E-0 TA5046_3885 Phaseolus_vulgaris_release_2 65808 67002 UBA-like [Medicago truncatula (Barrel medic)] asmbl_11857 Vigna_unguiculata 65951 67042 NA TA58707_3847 Glycine_max_release_2 66006 67253 UBA-like [Medicago truncatula (Barrel medic)] TC241193 GMGI.071508 66006 67253 similar to UniRef100_A7PM76 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (38%) BI967232 Glycine_max_release_2 66170 67203 UBA-like [Medicago truncatula (Barrel medic)] AV417590 LJGI.070108 66745 67090 similar to UniRef100_A7PM76 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (19%) AV768315 Lotus_japonicus_release_1 66699 67155 UBA-like [Medicago truncatula (Barrel medic)] TC32114 LJGI.070108 66699 67275 similar to UniRef100_Q76KU6 Cluster: DNA methyltransferase, n = 1, Nicotiana tabacum|Rep: DNA methyltransferase - Nicotiana tabacum (Common tobacco), partial (20%) TA1535_34305 Lotus_japonicus_release_1 66745 67277 UBA-like [Medicago truncatula (Barrel medic)] TA2793_47247 Lotus_corniculatus_release_1 66745 67277 DNA methyltransferase related cluster AV768911 Lotus_japonicus_release_1 66943 67155 Ubiquitin-associated [Medicago truncatula (Barrel medic)] CB540531 Phaseolus_vulgaris 73267 73561 UniRef100_A7PM74 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PM74_VITVI 5.00E−27 BE347690 GMGI.071508 73509 73770 similar to UniRef100_Q5VQL1-2 Cluster: Isoform 2 of Q5VQL1; n = 1; Oryza sativa Japonica Group|Rep: Isoform 2 of Q5VQL1 - Oryza sativa subsp. japonica (Rice) = partial (5%) BE347690 Glycine_max_release_2 73509 73822 WW/Rsp5/WWP; Helicase = C- terminal [Medicago truncatula (Barrel medic)] BE608496 GMGI.071508 73444 73947 similar to UniRef100_A7PM74 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (16%) AI416763 GMGI.071508 74073 74520 similar to UniRef100_Q9SP26 Cluster: P72 DEAD box protein; n = 1; Pisum sativum|Rep: P72 DEAD box protein - Pisum sativum (Garden pea) = partial (16%) AI416763 Glycine_max_release_2 74073 74743 ATP-dependent RNA helicase- like protein DB10 [Nicotiana sylvestris (Wood tobacco)] BW615083 LJGI.070108 74256 74855 similar to UniRef100_A7PM74 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (24%) TA8332_34305 Lotus_japonicus_release_1 74256 75446 WW/Rsp5/WWP, Helicase, C- terminal [Medicago truncatula (Barrel medic)] TC27807 LJGI.070108 74343 75446 similar to UniRef100_Q9SP26 Cluster: P72 DEAD box protein, n = 1, Pisum sativum|Rep: P72 DEAD box protein - Pisum sativum (Garden pea), partial (34%) asmbl_11858 Vigna_unguiculata 75228 75500 NA TA60825_3847 Glycine_max_release_2 74963 75981 P72 DEAD box protein [Pisum sativum (Garden pea)] TC249436 GMGI.071508 74985 75966 similar to UniRef100_Q9SP26 Cluster: P72 DEAD box protein; n = 1; Pisum sativum|Rep: P72 DEAD box protein - Pisum sativum (Garden pea) = partial (12%) TC269249 GMGI.071508 86882 87576 similar to UniRef100_A7PM72 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (42%) TA64136_3847 Glycine_max_release_2 86882 89066 Putative phosphate/phosphoenolpyruvate translocator [Arabidopsis thaliana (Mouse-ear cress)] CO982132 Glycine_max_release_2 87225 91497 Phosphate/phosphoenolpyruvate translocator [Nicotiana tabacum (Common tobacco)] TC274531 GMGI.071508 87225 91497 similar to UniRef100_A4UTS3 Cluster: Chloroplast phosphoenolpyruvate/phosphate translocator; n = 1; Pisum sativum|Rep: Chloroplast phosphoenolpyruvate/phosphate translocator - Pisum sativum (Garden pea) = partial (53%) Pvcon2802 Phaseolus_vulgaris 87119 92616 UniRef100_A9PD12 Putative uncharacterized protein n = 1 Tax = Populus trichocarpa RepID = A9PD12_POPTR 1.00E−121 TA4406_3885 Phaseolus_vulgaris_release_2 89055 92616 Phosphate/phosphoenolpyruvate translocator [Nicotiana tabacum (Common tobacco)] TA74766_3847 Glycine_max_release_2 91397 92725 Phosphoenolpyruvate/phosphate translocator [Mesembryanthemum crystallinum (Common ice plant)] TC265023 GMGI.071508 91686 92725 similar to UniRef100_A7PM71 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (15%) M0205928 SEQ. 92718 92334 SEQ ID NO: 3 LISTING BG406195 GMGI.071508 107039 107366 (SEQ ID NO: 13) BG406195 Glycine_max_release_2 107039 107375 NA M0101742 SEQ. 112189 113483 SEQ ID NO: 5 LISTING BG550728 GMGI.071508 112663 113757 weakly similar to UniRef100_A7PM60 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (13%) BG550728 Glycine_max_release_2 112663 113867 Receptor-like serine/threonine kinase [Arabidopsis thaliana (Mouse-ear cress)] CV535605 Phaseolus_vulgaris 112548 113982 UniRef100_A7PM60 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PM60_VITVI 9.00E−79 M0129138 SEQ. 114532 113494 SEQ ID NO: 4 LISTING BU551345 Glycine_max_release_2 115956 116339 (SEQ ID NO: 16) TA58315_3847 Glycine_max_release_2 118318 120087 NA TC236438 GMGI.071508 118318 120087 NA BE611751 Glycine_max_release_2 119165 119645 NA BE611751 GMGI.071508 119229 119645 NA TA70371_3847 Glycine_max_release_2 137417 137864 Hypothetical protein [Medicago truncatula (Barrel medic)] TC267549 GMGI.071508 137417 137864 similar to UniRef100_Q9FI64 Cluster: Genomic DNA = chromosome 5 = TAC clone: K21I16; n = 1; Arabidopsis thaliana|Rep: Genomic DNA = chromosome 5 = TAC clone: K21I16 - Arabidopsis thaliana (Mouse- ear cress) = partial (43%) BG156330 GMGI.071508 155872 156903 similar to UniRef100_A7PM41 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 2; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (23%) BG156330 Glycine_max_release_2 155872 157058 WD40-like [Medicago truncatula (Barrel medic)] Pvcon10326 Phaseolus_vulgaris 155691 157835 UniRef100_A7PM41 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PM41_VITVI 3.00E−93 CD397113 Glycine_max_release_2 157474 157813 NA TA12653_34305 Lotus_japonicus_release_1 159489 161341 NADP-specific isocitrate dehydrogenase [Lupinus albus (White lupin)] TC27381 LJGI.070108 159489 161341 similar to UniRef100_Q7Y0W7 Cluster: NADP-specific isocitrate dehydrogenase, n = 1, Lupinus albus|Rep: NADP- specific isocitrate dehydrogenase - Lupinus albus (White lupin), partial (25%) DT084057 Glycine_soja_release_2 161638 162192 NADP-specific isocitrate dehydrogenase [Lupinus albus (White lupin)] BE661051 Glycine_max_release_2 170271 172034 Cyclin-like F-box [Medicago truncatula (Barrel medic)] TA11305_34305 Lotus_japonicus_release_1 170700 172307 Cyclin-like F-box [Medicago truncatula (Barrel medic)] TC34049 LJGI.070108 170700 172307 similar to UniRef100_A7PF14 Cluster: Chromosome chr11 scaffold_13, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr11 scaffold_13, whole genome shotgun sequence - Vitis vinifera (Grape), partial (32%) NP7256876 MTGI.071708 171929 173188 GB|AC157983.16|ABE86510.1 Cyclin-like F-box TA68495_3847 Glycine_max_release_2 194920 195696 Oleosin [Sesamum indicum (Oriental sesame) (Gingelly)] TC265354 GMGI.071508 194920 195696 weakly similar to UniRef100_P29530 Cluster: P24 oleosin isoform A; n = 1; Glycine max|Rep: P24 oleosin isoform A - Glycine max (Soybean) = partial (40%) BE658264 Glycine_max_release_2 195176 195925 Oleosin [Sesamum indicum (Oriental sesame) (Gingelly)] CV539661 Phaseolus_vulgaris 217885 218101 No significant hit (e−20) CA912681 Phaseolus_coccineus_release_2 220374 220748 Arabidopsis thaliana genomic DNA, chromosome 3, P1 clone: MGF10 [Arabidopsis thaliana (Mouse-ear cress)] CA785107 Glycine_soja_release_2 221393 221885 NA TC276537 GMGI.071508 221407 222104 weakly similar to UniRef100_Q4RYK7 Cluster: Chromosome 3 SCAF14975 = whole genome shotgun sequence; n = 1; Tetraodon nigroviridis|Rep: Chromosome 3 SCAF14975 = whole genome shotgun sequence - Tetraodon nigroviridis (Green puffer) = partial (21%) TA71044_3847 Glycine_max_release_2 221407 222133 NA CD406643 Glycine_max_release_2 222113 222297 NA AV416316 LJGI.070108 223773 223869 similar to UniRef100_A7PM35 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (9%) EC911350 Phaseolus_vulgaris 224587 225958 UniRef100_A5C233 Putative uncharacterized protein n = 1 Tax = Vitis vinifera RepID = A5C233_VITVI 3.00E−77 BU760697 GMGI.071508 224857 225965 similar to UniRef100_A7PM35 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (22%) BU760697 Glycine_max_release_2 224857 226145 Protein At5g19130 [Arabidopsis thaliana (Mouse- ear cress)] TC119982 MTGI.071708 224248 226812 Gaa1-like, GPI transamidase component CV541515 Phaseolus_vulgaris 225934 226374 UniRef100_A7PM35 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PM35_VITVI 2.00E−34 TA76349_3847 Glycine_max_release_2 226118 226768 Protein At5g19130 [Arabidopsis thaliana (Mouse- ear cress)] TA12045_47247 Lotus_corniculatus_release_1 226354 226789 GPAA1-like protein related cluster TA13675_34305 Lotus_japonicus_release_1 226354 226789 Protein At5g19130 [Arabidopsis thaliana (Mouse- ear cress)] TC29330 LJGI.070108 226354 226789 similar to UniRef100_A7PM35 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (13%) NP7254537 MTGI.071708 233411 237212 GB|AC152349.11|ABP03404.1 Protein of unknown function DUF266, plant EH256962 GMGI.071508 235306 237649 similar to UniRef100_A7PM54 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (33%) CX708677 Glycine_max_release_2 247269 248145 NA BW599077 LJGI.070108 255475 261945 similar to UniRef100_A7QD90 Cluster: Peptidyl-prolyl cis- trans isomerase, n = 1, Vitis vinifera|Rep: Peptidyl-prolyl cis-trans isomerase - Vitis vinifera (Grape), partial (18%) BW625918 LJGI.070108 257810 262980 similar to UniRef100_Q93YQ8 Cluster: Peptidyl-prolyl cis- trans isomerase, n = 1, Arabidopsis thaliana|Rep: Peptidyl-prolyl cis-trans isomerase - Arabidopsis thaliana (Mouse-ear cress), partial (32%) DT083826 Glycine_soja_release_2 260886 261121 NA CB063628 GMGI.071508 271592 271900 similar to UniRef100_A7PM52 Cluster: Chromosome chr14 scaffold_21 whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: = partial (2%) CB063628 Glycine_max_release_2 271592 271928 NA TA5835_34305 Lotus_japonicus_release_1 273868 275906 Vegetative cell wall protein gp1-like [Oryza sativa (japonica cultivar-group)] TC32024 LJGI.070108 275152 275906 similar to UniRef100_A7PM52 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (9%) TC252667 GMGI.071508 275739 276506 similar to UniRef100_A7PM52 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (12%) AW311416 Glycine_max_release_2 276269 276455 NA WmFPC_Contig850 99810 475910 NA CV534998 Phaseolus_vulgaris 288050 288585 UniRef100_A7PM50 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PM50_VITVI 6.00E−39 TA75806_3847 Glycine_max_release_2 288290 290376 Arabidopsis thaliana genomic DNA = chromosome 3 = P1 clone: MGF10 [Arabidopsis thaliana (Mouse-ear cress)] TC276120 GMGI.071508 288290 290376 similar to UniRef100_A7PM50 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (62%) BI786388 GMGI.071508 291666 292088 similar to UniRef100_A7PM49 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (7%) BI786388 Glycine_max_release_2 291666 292099 NA TA63308_3847 Glycine_max_release_2 291633 294397 NA TC243765 GMGI.071508 293681 294426 weakly similar to UniRef100_Q0JDM0 Cluster: Os04g0394300 protein; n = 1; Oryza sativa Japonica Group|Rep: Os04g0394300 protein - Oryza sativa subsp. japonica (Rice) = partial (3%) TA6412_34305 Lotus_japonicus_release_1 293803 294412 NA TC24112 LJGI.070108 293803 294412 NA CA899930 Phaseolus_coccineus_release_2 294054 294263 NA TA3887_3886 Phaseolus_coccineus_release_2 302301 303033 Hypothetical protein MJH23.3 [Arabidopsis thaliana (Mouse- ear cress)] AW705271 Glycine_max_release_2 302299 303855 Hypothetical protein MJH23.3 [Arabidopsis thaliana (Mouse- ear cress)] TC237313 GMGI.071508 303227 306007 similar to UniRef100_A7PM30 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (54%) TA61594_3847 Glycine_max_release_2 303227 306056 Similarity to RNA binding protein [Arabidopsis thaliana (Mouse-ear cress)] asmbl_11859 Vigna_unguiculata 303952 305921 NA toGm05 DAGchainer 30059 580791 Ks0.2335 BU544029 Glycine_max_release_2 305220 305762 NA TC23280 LJGI.070108 305373 305839 similar to UniRef100_A7PM30 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (17%) AI461058 Glycine_max_release_2 305614 305834 NA BE555571 Glycine_max_release_2 305656 306011 NA asmbl_11860 Vigna_unguiculata 319622 320527 NA EV270366 GMGI.071508 319893 320575 similar to UniRef100_P15792 Cluster: Protein kinase PVPK- 1; n = 1; Phaseolus vulgaris|Rep: Protein kinase PVPK-1 - Phaseolus vulgaris (Kidney bean) (French bean) = partial (34%) J04555 Phaseolus_vulgaris_release_2 318937 322709 Protein kinase PVPK-1 [Phaseolus vulgaris (Kidney bean) (French bean)] TA11578_34305 Lotus_japonicus_release_1 320355 322024 Protein kinase PVPK-1 [Phaseolus vulgaris (Kidney bean) (French bean)] TC35252 LJGI.070108 320355 322381 homologue to UniRef100_P15792 Cluster: Protein kinase PVPK-1, n = 1, Phaseolus vulgaris|Rep: Protein kinase PVPK-1 - Phaseolus vulgaris (Kidney bean) (French bean), partial (48%) Pvcon4227 Phaseolus_vulgaris 320098 322709 UniRef100_P15792 Protein kinase PVPK-1 n = 1 Tax = Phaseolus vulgaris RepID = KPK1_PHAVU E-0 CA900819 Phaseolus_coccineus_release_2 325129 325547 Sucrase-like protein [Arabidopsis thaliana (Mouse- ear cress)] CA900820 Phaseolus_coccineus_release_2 325119 328122 AT3g27570/MMJ24_12 [Arabidopsis thaliana (Mouse- ear cress)] TC269193 GMGI.071508 325136 329359 weakly similar to UniRef100_A7PM27 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (47%) TA4354_3885 Phaseolus_vulgaris_release_2 325476 329154 AT5g40510/MNF13_30 [Arabidopsis thaliana (Mouse- ear cress)] asmbl_11861 Vigna_unguiculata 326881 329154 NA CF920945 Glycine_max_release_2 326967 329359 AT3g27570/MMJ24_12 [Arabidopsis thaliana (Mouse- ear cress)] SATT723 337605 337828 Satt723 ePCR 337605 337828 Map3.0 SSR L/Gm19 cM: 1.5 TC244213 GMGI.071508 354373 354996 similar to UniRef100_A7PL06 Cluster: Chromosome chr7 scaffold_20 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr7 scaffold_20 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (17%) BU090380 Glycine_max_release_2 354683 354871 NA BP058294 Lotus_japonicus_release_1 355950 356319 Protein ycf2 [Lotus japonicus] Pvcon2444 Phaseolus_vulgaris 354593 360732 UniRef100_A7PL07 Chromosome chr7 scaffold_20, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PL07_VITVI 1.00E−144 asmbl_11862 Vigna_unguiculata 359273 359896 NA CA800649 Glycine_max_release_2 377994 379933 AT3g01590/F4P13_13 [Arabidopsis thaliana (Mouse- ear cress)] TC245493 GMGI.071508 377994 381638 similar to UniRef100_A7PM21 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (96%) CO984617 Glycine_max_release_2 379899 381537 At5g14500 [Arabidopsis thaliana (Mouse-ear cress)] M0114388 SEQ. 381308 380486 SEQ ID NO: 2 LISTING AW704585 Glycine_max_release_2 381210 381673 At5g14500 [Arabidopsis thaliana (Mouse-ear cress)] TC248588 GMGI.071508 383419 383857 NA asmbl_11863 Vigna_unguiculata 383428 384088 NA TC126554 MTGI.071708 383593 384668 weakly similar to UniRef100_Q940C3 Cluster: AT3g27530/MMJ24_7, n = 2, Arabidopsis thaliana|Rep: AT3g27530/MMJ24_7 - Arabidopsis thaliana (Mouse- ear cress), partial (38%) AJ002216 Pisum_sativum_release_2 384088 384751 Emb|CAA07228.1 [Arabidopsis thaliana (Mouse-ear cress)] BI702257 GMGI.071508 384067 384789 similar to UniRef100_Q940C3 Cluster: AT3g27530/MMJ24_7; n = 2; Arabidopsis thaliana|Rep: AT3g27530/MMJ24_7 - Arabidopsis thaliana (Mouse- ear cress) = partial (14%) BG451913 MTGI.071708 386353 388007 similar to UniRef100_Q9LT59 Cluster: Emb|CAA07228.1, n = 1, Arabidopsis thaliana|Rep: Emb|CAA07228.1 - Arabidopsis thaliana (Mouse- ear cress), partial (19%) CV533025 Phaseolus_vulgaris 388647 389345 UniRef100_UPI000016357E GC6 (GOLGIN CANDIDATE 6) binding/protein transporter Tax = n = 1 RepID = UPI000016357E 6.00E−27 AV777312 LJGI.070108 389152 391279 similar to UniRef100_Q9LT59 Cluster: Emb|CAA07228.1, n = 1, Arabidopsis thaliana|Rep: Emb|CAA07228.1 - Arabidopsis thaliana (Mouse- ear cress), partial (19%) BM187543 GMGI.071508 394984 395407 similar to UniRef100_A7PM13 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (36%) BM187543 Glycine_max_release_2 394984 395559 Gb|AAF01546.1 [Arabidopsis thaliana (Mouse-ear cress)] DN652256 LJGI.070108 395487 395708 similar to UniRef100_A7P4B1 Cluster: Chromosome chr1 scaffold_5, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr1 scaffold_5, whole genome shotgun sequence - Vitis vinifera (Grape), partial (19%) DT044393 Arachis_hypogaea_release_5 395462 395746 Cluster: Hypothetical protein T23K23.27, n = 1, Arabidopsis thaliana|Rep: Hypothetical protein T23K23.27 - Arabidopsis thaliana (Mouse- ear cress) FD789910 Phaseolus_vulgaris 395555 395927 UniRef100_A7P4B1 Chromosome chr1 scaffold_5, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7P4B1_VITVI 2.00E−59 EH259382 GMGI.071508 395577 396156 similar to UniRef100_A7PM13 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (34%) TA69305_3847 Glycine_max_release_2 403237 404175 NA TC243910 GMGI.071508 403237 404175 similar to UniRef100_A7PM14 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (5%) CA785084 Glycine_soja_release_2 403526 404055 NA CV541170 Phaseolus_vulgaris 404688 406556 UniRef100_Q9LT57 Emb|CAB45506.1 n = 1 Tax = Arabidopsis thaliana RepID = Q9LT57_ARATH 1.00E−113 BF071095 GMGI.071508 406510 407127 similar to UniRef100_Q9LT57 Cluster: Emb|CAB45506.1; n = 1; Arabidopsis thaliana|Rep: Emb|CAB45506.1 - Arabidopsis thaliana (Mouse- ear cress) = partial (8%) BF071095 Glycine_max_release_2 406527 407127 NA BM270669 Glycine_max_release_2 409910 410532 NA BM270669 GMGI.071508 410045 410532 similar to UniRef100_A7PM16 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (9%) BG550673 GMGI.071508 421541 422250 similar to UniRef100_A7PM12 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (26%) BG550673 Glycine_max_release_2 421541 422354 Hypothetical protein F18O22_260 [Arabidopsis thaliana (Mouse-ear cress)] BU551363 Glycine_max_release_2 422150 422745 NA CD407423 Glycine_max_release_2 423719 423842 NA M0205350 SEQ Listing 424095 423776 SEQ ID NO: 1 EV270239 GMGI.071508 425649 426181 similar to UniRef100_Q0WVR7 Cluster: TRNA synthase-like protein; n = 1; Arabidopsis thaliana|Rep: TRNA synthase-like protein - Arabidopsis thaliana (Mouse- ear cress) = partial (5%) BI424448 GMGI.071508 451332 451679 similar to UniRef100_P82353 Cluster: Non-specific lipid- transfer protein 2; n = 1; Prunus armeniaca|Rep: Non-specific lipid-transfer protein 2 - Prunus armeniaca (Apricot) = partial (68%) TA49179_3847 Glycine_max_release_2 451332 451827 Nonspecific lipid-transfer protein 2 [Prunus armeniaca (Apricot)] TC252453 GMGI.071508 451397 451828 weakly similar to UniRef100_Q43681 Cluster: Probable non-specific lipid- transfer protein AKCS9 precursor; n = 1; Vigna unguiculata|Rep: Probable non- specific lipid-transfer protein AKCS9 precursor - Vigna unguiculata (Cowpea) = partial (86%) BE609938 Glycine_max_release_2 451607 451756 Probable lipid transfer protein family protein [Tamarix androssowii] BQ612382 Glycine_max_release_2 451777 452217 NA NS0102027 466228 466889 Pvcon7917 Phaseolus_vulgaris 466120 467338 UniRef100_A5C9E2 Putative uncharacterized protein n = 1 Tax = Vitis vinifera RepID = A5C9E2_VITVI 6.00E−44 asmbl_11864 Vigna_unguiculata 467520 468191 NA TA49596_3847 Glycine_max_release_2 470086 472059 Methionine aminopeptidase 2B [Arabidopsis thaliana (Mouse- ear cress)] TC255857 GMGI.071508 470086 476828 homologue to UniRef100_A7PXX3 Cluster: Methionine aminopeptidase; n = 1; Vitis vinifera|Rep: Methionine aminopeptidase - Vitis vinifera (Grape) = partial (91%) FD792539 Phaseolus_vulgaris 472774 475674 UniRef100_A7PXX3 Methionine aminopeptidase n = 1 Tax = Vitis vinifera RepID = A7PXX3_VITVI 5.00E−56 TA3829_3848 Glycine_soja_release_2 471918 476623 Methionine aminopeptidase 2B [Arabidopsis thaliana (Mouse- ear cress)] BU765955 Glycine_max_release_2 472787 475846 Methionine aminopeptidase 2B [Arabidopsis thaliana (Mouse- ear cress)] EG530516 Arachis_hypogaea_release_5 472835 476690 Cluster: Methionine aminopeptidase 2B, n = 1, Arabidopsis thaliana|Rep: Methionine aminopeptidase 2B - Arabidopsis thaliana (Mouse- ear cress) AV425234 LJGI.070108 475562 475924 homologue to UniRef100_A7PXX3 Cluster: Methionine aminopeptidase, n = 1, Vitis vinifera|Rep: Methionine aminopeptidase - Vitis vinifera (Grape), partial (22%) TA49598_3847 Glycine_max_release_2 474794 476709 Methionine aminopeptidase 2B [Arabidopsis thaliana (Mouse- ear cress)] FD797260 Phaseolus_vulgaris 475768 476654 UniRef100_A7PXX3 Methionine aminopeptidase n = 1 Tax = Vitis vinifera RepID = A7PXX3_VITVI 6.00E−55 BE823844 Glycine_max_release_2 475751 476828 Methionine aminopeptidase 2B [Arabidopsis thaliana (Mouse- ear cress)] BG726070 Glycine_max_release_2 476668 476807 NA BQ080926 GMGI.071508 480002 480636 similar to UniRef100_A7PY54 Cluster: Chromosome chr15 scaffold_37 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr15 scaffold_37 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (39%) TA69442_3847 Glycine_max_release_2 480002 481069 Hypothetical protein F22I13.40 [Arabidopsis thaliana (Mouse- ear cress)] TC262427 GMGI.071508 480002 481069 similar to UniRef100_A7P8Q6 Cluster: Chromosome chr3 scaffold_8 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr3 scaffold_8 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (20%) BU548976 Glycine_max_release_2 481474 481970 Multi antimicrobial extrusion protein MatE [Medicago truncatula (Barrel medic)] CX547082 Glycine_max_release_2 481345 482173 Multi antimicrobial extrusion protein MatE [Medicago truncatula (Barrel medic)] TC236122 GMGI.071508 481300 482612 NA TA57759_3847 Glycine_max_release_2 481300 482627 Multi antimicrobial extrusion protein MatE [Medicago truncatula (Barrel medic)] AV420909 LJGI.070108 481846 482201 weakly similar to UniRef100_A7QTE8 Cluster: Chromosome undetermined scaffold_167, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome undetermined scaffold_167, whole genome shotgun sequence - Vitis vinifera (Grape), partial (24%) AW597322 Glycine_max_release_2 481965 482825 Multi antimicrobial extrusion protein MatE [Medicago truncatula (Barrel medic)] BM270610 Glycine_max_release_2 482034 483008 Multi antimicrobial extrusion protein MatE [Medicago truncatula (Barrel medic)] BI972603 GMGI.071508 482632 483190 weakly similar to UniRef100_A7P3G6 Cluster: Chromosome chr1 scaffold_5 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr1 scaffold_5 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (20%) BI972603 Glycine_max_release_2 482632 484113 Multi antimicrobial extrusion protein MatE [Medicago truncatula (Barrel medic)] TA66198_3847 Glycine_max_release_2 482595 484230 Multi antimicrobial extrusion protein MatE [Medicago truncatula (Barrel medic)] TC253566 GMGI.071508 482648 484405 weakly similar to UniRef100_A7QTE8 Cluster: Chromosome undetermined scaffold_167 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome undetermined scaffold_167 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (44%) asmbl_11865 Vigna_unguiculata 482937 484289 NA BG881371 Glycine_max_release_2 483075 484230 Multi antimicrobial extrusion protein MatE [Medicago truncatula (Barrel medic)] WmFPC_Contig7443 384071 598745 NA AW695419 MTGI.071708 491367 494466 similar to UniRef100_A7PU69 Cluster: Chromosome chr7 scaffold_31, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr7 scaffold_31, whole genome shotgun sequence - Vitis vinifera (Grape), partial (11%) BF645755 MTGI.071708 494870 497474 similar to UniRef100_A7PU69 Cluster: Chromosome chr7 scaffold_31, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr7 scaffold_31, whole genome shotgun sequence - Vitis vinifera (Grape), partial (14%) BE475242 GMGI.071508 497000 497327 similar to UniRef100_A7NWE7 Cluster: Chromosome chr5 scaffold_2 whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: = partial (1%) BE475242 Glycine_max_release_2 497000 497549 Hypothetical protein At3g23590/MDB19_8 [Arabidopsis thaliana (Mouse- ear cress)] BW611072 LJGI.070108 497387 497795 similar to UniRef100_A7PU69 Cluster: Chromosome chr7 scaffold_31, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr7 scaffold_31, whole genome shotgun sequence - Vitis vinifera (Grape), partial (10%) BQ613050 Glycine_max_release_2 497409 498014 ORF protein [Arabidopsis thaliana (Mouse-ear cress)] CV541244 Phaseolus_vulgaris 500143 500464 UniRef100_A9PGX2 Putative uncharacterized protein n = 1 Tax = Populus trichocarpa RepID = A9PGX2_POPTR 3.00E−28 CX856527 Glycine_max_release_2 501517 501735 NA BG839076 Glycine_max_release_2 503126 505209 F2P3.12 protein [Arabidopsis thaliana (Mouse-ear cress)] FD790090 Phaseolus_vulgaris 503370 505191 No significant hit (e−20) TC236383 GMGI.071508 503107 505675 similar to UniRef100_O82505 Cluster: Elongation factor Ts; n = 1; Arabidopsis thaliana|Rep: Elongation factor Ts - Arabidopsis thaliana (Mouse- ear cress) = partial (32%) TA56246_3847 Glycine_max_release_2 503107 505848 Ethylene-responsive elongation factor EF-Ts precursor [Lycopersicon esculentum (Tomato)] TC239475 GMGI.071508 503126 506560 similar to UniRef100_Q9SWW0 Cluster: Ethylene-responsive elongation factor EF-Ts precursor; n = 1; Solanum lycopersicum|Rep: Ethylene-responsive elongation factor EF-Ts precursor - Solanum lycopersicum (Tomato) (Lycopersicon esculentum) = partial (74%) TA56245_3847 Glycine_max_release_2 505512 506546 Ethylene-responsive elongation factor EF-Ts precursor [Lycopersicon esculentum (Tomato)] BG839060 Glycine_max_release_2 505661 506530 At4g11120 [Arabidopsis thaliana (Mouse-ear cress)] CV543527 Phaseolus_vulgaris_release_2 508539 508771 Eukaryotic translation initiation factor 5 [Phaseolus vulgaris (Kidney bean) (French bean)] CD393454 Glycine_max_release_2 510651 511000 Ribosomal protein L22 [Glycine max (Soybean)] TC245517 GMGI.071508 510651 511270 homologue to UniRef100_O48879 Cluster: Ribosomal protein L22; n = 1; Glycine max|Rep: Ribosomal protein L22 - Glycine max (Soybean) = partial (80%) asmbl_11866 Vigna_unguiculata 510868 511269 NA TA51206_3847 Glycine_max_release_2 510702 512712 Ribosomal protein L22 [Glycine max (Soybean)] TC249077 GMGI.071508 510771 512771 homologue to UniRef100_O48879 Cluster: Ribosomal protein L22; n = 1; Glycine max|Rep: Ribosomal protein L22 - Glycine max (Soybean) = partial (98%) BG316244 Glycine_max_release_2 511015 512722 Ribosomal protein L22 [Glycine max (Soybean)] BQ155270 MTGI.071708 513084 514936 similar to UniRef100_A7PR59 Cluster: Chromosome chr14 scaffold_26, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_26, whole genome shotgun sequence - Vitis vinifera (Grape), partial (52%) TC30151 LJGI.070108 514647 516395 similar to UniRef100_A7PR59 Cluster: Chromosome chr14 scaffold_26, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_26, whole genome shotgun sequence - Vitis vinifera (Grape), partial (29%) BP044357 Lotus_japonicus_release_1 514647 516409 S-locus protein 8 [Brassica campestris (Field mustard)] CB540591 Phaseolus_vulgaris 514839 516355 No significant hit (e−20) TA65114_3847 Glycine_max_release_2 523413 524053 At1g22990/F19G10_22 [Arabidopsis thaliana (Mouse- ear cress)] TC259745 GMGI.071508 523413 524067 similar to UniRef100_A7P3I8 Cluster: Chromosome chr1 scaffold_5 = whole genome shotgun sequence; n = 2; Vitis vinifera|Rep: Chromosome chr1 scaffold_5 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (56%) TA4332_47247 Lotus_corniculatus_release_1 529321 530051 Actin-11 related cluster TA6031_34305 Lotus_japonicus_release_1 529321 530051 Actin [Striga asiatica] TC32457 LJGI.070108 529321 530051 homologue to UniRef100_P30167 Cluster: Actin-58, n = 1, Solanum tuberosum|Rep: Actin-58 - Solanum tuberosum (Potato), partial (39%) AW351005 Glycine_max_release_2 529380 530095 Actin [Striga asiatica] TA43521_3847 Glycine_max_release_2 529306 530175 Actin-11 [Arabidopsis thaliana (Mouse-ear cress)] asmbl_11867 Vigna_unguiculata 529342 530189 NA AU240079 LJGI.070108 529747 530013 homologue to UniRef100_P93372 Cluster: Actin-66, n = 1, Nicotiana tabacum|Rep: Actin-66- Nicotiana tabacum (Common tobacco), partial (25%) AU240079 Lotus_japonicus_release_1 529747 530039 Actin-11 [Arabidopsis thaliana (Mouse-ear cress)] EE127018 Arachis_hypogaea_release_5 529933 530285 Cluster: Hypothetical protein, n = 1, Oryza sativa (indica cultivar-group)|Rep: Hypothetical protein - Oryza sativa subsp. indica (Rice) TC240040 GMGI.071508 529306 531078 homologue to UniRef100_P02581 Cluster: Actin-1; n = 1; Glycine max|Rep: Actin-1 - Glycine max (Soybean) = complete AW666288 Glycine_max_release_2 529980 530789 Actin [Phaseolus acutifolius (Tepary bean)] TA43509_3847 Glycine_max_release_2 529888 530911 Actin [Glycine max (Soybean)] TA6074_34305 Lotus_japonicus_release_1 530031 531095 Actin-1 [Sorghum bicolor (Sorghum) (Sorghum vulgare)] TC26188 LJGI.070108 530031 531095 homologue to UniRef100_A1Y2A0 Cluster: Actin, n = 1, Aegiceras corniculatum|Rep: Actin - Aegiceras corniculatum, partial (81%) BM142797 Glycine_max_release_2 530212 531095 Actin [Trifolium pratense (Red clover)] BP036880 Lotus_japonicus_release_1 530235 531095 Actin/actin-like [Medicago truncatula (Barrel medic)] AW349632 Glycine_max_release_2 533113 533701 NA AI900119 Glycine_max_release_2 533044 534995 NA TA51800_3847 Glycine_max_release_2 533054 535063 NA TC241826 GMGI.071508 533055 535063 similar to UniRef100_Q2Z1Y5 Cluster: Pm52 protein; n = 1; Prunus mume|Rep: Pm52 protein - Prunus mume (Japanese flowering apricot) = partial (73%) BU494245 LJGI.070108 533191 534994 weakly similar to UniRef100_Q2Z1Y5 Cluster: Pm52 protein, n = 1, Prunus mume|Rep: Pm52 protein - Prunus mume (Japanese flowering apricot), partial (59%) AI440735 Glycine_max_release_2 534517 535020 NA AI440735 GMGI.071508 534522 535020 similar to UniRef100_Q2Z1Y5 Cluster: Pm52 protein; n = 1; Prunus mume|Rep: Pm52 protein - Prunus mume (Japanese flowering apricot) = partial (41%) TC250013 GMGI.071508 536842 537680 UniRef100_Q8L7J4 Cluster: Pyruvate kinase; n = 1; Glycine max|Rep: Pyruvate kinase - Glycine max (Soybean) = partial (29%) TA10574_343051 Lotus_japonicus_release_1 537149 537628 Pyruvate kinase [Glycine max (Soybean)] TC26632 LJGI.070108 537149 537628 homologue to UniRef100_Q42806 Cluster: Pyruvate kinase, cytosolic isozyme, n = 1, Glycine max|Rep: Pyruvate kinase, cytosolic isozyme - Glycine max (Soybean), partial (26%) CV536725 Phaseolus_vulgaris_release_2 537147 537846 Pyruvate kinase = cytosolic isozyme [Glycine max (Soybean)] asmbl_11868 Vigna_unguiculata 537127 538325 NA TC25282 LJGI.070108 537149 538489 homologue to UniRef100_Q8L7J4 Cluster: Pyruvate kinase, n = 1, Glycine max|Rep: Pyruvate kinase - Glycine max (Soybean), partial (29%) TA47094_3847 Glycine_max_release_2 536842 539314 Pyruvate kinase [Glycine max (Soybean)] Pvcon4373 Phaseolus_vulgaris 537147 539113 UniRef100_Q42806 Pyruvate kinase, cytosolic isozyme n = 1 Tax = Glycine max RepID = KPYC_SOYBN E-0 TC124922 MTGI.071708 537491 538783 homologue to UniRef100_Q42806 Cluster: Pyruvate kinase, cytosolic isozyme, n = 1, Glycine max|Rep: Pyruvate kinase, cytosolic isozyme - Glycine max (Soybean), partial (64%) BF598352 Glycine_soja_release_2 538308 538971 Pyruvate kinase [Citrus sinensis (Sweet orange)] BG044770 Glycine_soja_release_2 538624 539149 Pyruvate kinase [Citrus sinensis (Sweet orange)] TC249941 GMGI.071508 538549 539314 UniRef100_Q8L7J4 Cluster: Pyruvate kinase; n = 1; Glycine max|Rep: Pyruvate kinase - Glycine max (Soybean) = partial (37%) BE608312 Glycine_max_release_2 542536 544875 Hypothetical protein [Arabidopsis thaliana (Mouse- ear cress)] TC253996 GMGI.071508 542045 546856 similar to UniRef100_A7QNQ5 Cluster: Chromosome undetermined scaffold_133 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome undetermined scaffold_133 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (80%) TC258772 GMGI.071508 548268 548805 NA CV533614 Phaseolus_vulgaris 548540 548638 No significant hit TA57756_3847 Glycine_max_release_2 548268 551375 Putative microtubule-severing protein subunit [Oryza sativa (japonica cultivar-group)] TC239891 GMGI.071508 548323 551375 similar to UniRef100_A7QNQ6 Cluster: Chromosome undetermined scaffold_133 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome undetermined scaffold_133 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (12%) EH221990 GMGI.071508 550796 551633 weakly similar to UniRef100_A7QNQ6 Cluster: Chromosome undetermined scaffold_133 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome undetermined scaffold_133 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (7%) EV263369 GMGI.071508 552842 553615 similar to UniRef100_A8D2Q2 Cluster: ATP synthase protein 8; n = 1; Caranx ignobilis|Rep: ATP synthase protein 8 - Caranx ignobilis = partial (37%) BU964969 Glycine_max_release_2 556336 556943 NA BU964969 GMGI.071508 556494 556943 similar to UniRef100_Q9MYM4 Cluster: Lysosomal alpha-glucosidase precursor; n = 1; Bos taurus|Rep: Lysosomal alpha-glucosidase = partial (1%) EH221989 GMGI.071508 562783 563692 homologue to UniRef100_A7QNQ6 Cluster: Chromosome undetermined scaffold_133 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome undetermined scaffold_133 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (3%) AW831441 GMGI.071508 573069 573567 NA AW831441 Glycine_max_release_2 573069 573639 NA TA6761_34305 Lotus_japonicus_release_1 573706 580487 Sphingosine kinase [Lotus japonicus] TC20288 LJGI.070108 573706 580487 UniRef100_Q5KR50 Cluster: Sphingosine kinase, n = 1, Lotus japonicus|Rep: Sphingosine kinase - Lotus japonicus, complete TC122322 MTGI.071708 574490 580620 homologue to UniRef100_Q5KR50 Cluster: Sphingosine kinase, n = 1, Lotus japonicus|Rep: Sphingosine kinase - Lotus japonicus, partial (66%) BI701010 Glycine_max_release_2 577145 579375 Sphingosine kinase [Lotus japonicus] Pvcon3123 Phaseolus_vulgaris 577107 580468 UniRef100_Q5KR50 Sphingosine kinase n = 1 Tax = Lotus japonicus RepID = Q5KR50_LOTJA E-0 TA49258_3847 Glycine_max_release_2 579511 580791 Sphingosine kinase [Lotus japonicus] TC235674 GMGI.071508 579511 580791 homologue to UniRef100_Q5KR50 Cluster: Sphingosine kinase; n = 1; Lotus japonicus|Rep: Sphingosine kinase - Lotus japonicus = partial (26%) BI969866 Glycine_max_release_2 579600 580756 Sphingosine kinase [Lotus japonicus] EH043869 Arachis_stenosperma_release_5 579729 580660 Cluster: Sphingosine kinase, n = 1, Lotus japonicus|Rep: Sphingosine kinase - Lotus japonicus BQ786742 Glycine_max_release_2 580594 580719 NA BM108235 Glycine_max_release_2 581688 582006 NA AW508189 Glycine_max_release_2 581725 582244 Hypothetical protein [Arabidopsis thaliana (Mouse- ear cress)] TC238711 GMGI.071508 581688 582562 similar to UniRef100_A7QNQ7 Cluster: Chromosome undetermined scaffold_133 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome undetermined scaffold_133 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (50%) TA46155_3847 Glycine_max_release_2 581745 582556 Hypothetical protein [Arabidopsis thaliana (Mouse- ear cress)] AW278369 GMGI.071508 581988 582389 similar to UniRef100_A7QNQ7 Cluster: Chromosome undetermined scaffold_133 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome undetermined scaffold_133 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (44%) AW278369 Glycine_max_release_2 581988 582418 Hypothetical protein [Arabidopsis thaliana (Mouse- ear cress)] CD394810 Glycine_max_release_2 582134 582328 NA BG047332 Glycine_max_release_2 591288 592013 OSJNBb0065L13.3 protein [Oryza sativa (japonica cultivar-group)] TC272805 GMGI.071508 591358 592013 similar to UniRef100_A7NXM8 Cluster: Chromosome chr5 scaffold_2 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr5 scaffold_2 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (15%) BW599171 LJGI.070108 593399 593875 weakly similar to UniRef100_A7PT63 Cluster: Chromosome chr8 scaffold_29, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr8 scaffold_29, whole genome shotgun sequence - Vitis vinifera (Grape), partial (24%) BE057829 Glycine_max_release_2 606858 607008 NA TC275159 GMGI.071508 606858 607456 NA BE612118 GMGI.071508 615853 616253 weakly similar to UniRef100_A7GPV4 Cluster: Citrate transporter; n = 1; Bacillus cereus subsp. cytotoxis NVH 391-98|Rep: Citrate transporter - Bacillus cereus subsp. cytotoxis (strain NVH 391-98) = partial (5%) BE612118 Glycine_max_release_2 615869 616269 NA CA910895 Phaseolus_coccineus_release_2 622174 622531 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone: MPO12 [Arabidopsis thaliana (Mouse-ear cress)] BU763992 Glycine_max_release_2 625192 625591 NA TA51978_3847 Glycine_max_release_2 625330 626304 Putative ethylene-responsive protein [Oryza sativa (japonica cultivar-group)] TC236117 GMGI.071508 625330 626304 similar to UniRef100_A7PM86 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (43%) TC263881 GMGI.071508 625192 627651 similar to UniRef100_A7PM86 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (76%) TA51979_3847 Glycine_max_release_2 625252 627642 Putative ethylene response protein [Capsicum chinense (Scotch bonnet) (Bonnet pepper)] TC236300 GMGI.071508 625318 627642 similar to UniRef100_A7PM86 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (98%) CA910548 Phaseolus_coccineus_release_2 625559 627607 Putative ethylene response protein [Capsicum chinense (Scotch bonnet) (Bonnet pepper)] Pvcon5808 Phaseolus_vulgaris 625567 627610 UniRef100_A7PM86 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PM86_VITVI 2.00E−77 EV269595 GMGI.071508 627204 627569 similar to UniRef100_A7PM86 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (29%) BI273677 Glycine_max_release_2 637550 637816 NA BP049107 Lotus_corniculatus_release_1 647584 649419 Cinnamoyl CoA reductase-like protein related cluster TC258382 GMGI.071508 646415 652371 weakly similar to UniRef100_A7PM88 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (72%) TA50222_3847 Glycine_max_release_2 646722 652222 Cinnamoyl CoA reductase-like protein [Arabidopsis thaliana (Mouse-ear cress)] SATT495 650288 650531 Satt495 ePCR 650288 650531 Map3.0 SSR L/Gm19 cM: 2.7 AW099618 GMGI.071508 649276 652222 weakly similar to UniRef100_A7PM88 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (23%) TA50296_3847 Glycine_max_release_2 674409 676421 NA BQ629031 Glycine_max_release_2 674669 676494 NA BM520842 Glycine_soja_release_2 674685 676538 NA TC264557 GMGI.071508 674741 676494 NA BU765059 Glycine_max_release_2 674828 676698 NA BU765059 GMGI.071508 674925 676698 weakly similar to UniRef100_A7L4B0 Cluster: Protein kinase; n = 1; Carica papaya|Rep: Protein kinase - Carica papaya (Papaya) = partial (6%) TC264815 GMGI.071508 674409 678111 weakly similar to UniRef100_A7L4B0 Cluster: Protein kinase; n = 1; Carica papaya|Rep: Protein kinase - Carica papaya (Papaya) = partial (14%) asmbl_11869 Vigna_unguiculata 676473 676672 NA TA50295_3847 Glycine_max_release_2 674775 678957 NA Pvcon1987 Phaseolus_vulgaris 674506 679702 UniRef100_A7L4B0 Protein kinase n = 1 Tax = Carica papaya RepID = A7L4B0_CARPA 1.00E−127 BM528477 Glycine_max_release_2 676507 678111 NA TA11531_47247 Lotus_corniculatus_release_1 676692 678714 Protein kinase-like protein related cluster TA13031_343051 Lotus_japonicus_release_1 676692 678714 Hypothetical protein At5g14720 [Arabidopsis thaliana (Mouse-ear cress)] TC31122 LJGI.070108 676701 678714 similar to UniRef100_A7L4B0 Cluster: Protein kinase, n = 1, Carica papaya|Rep: Protein kinase - Carica papaya (Papaya), partial (14%) TC255388 GMGI.071508 679127 681361 homologue to UniRef100_A7PM90 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (44%) TC124284 MTGI.071708 679117 681419 homologue to UniRef100_A7PM90 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (48%) DV565290 Phaseolus_vulgaris 681368 681460 No significant hit (e−20) toGm05 DAGchainer 603011 803108 Ks0.2166 NP7265365 MTGI.071708 703588 713159 GB|AC124951.19|ABE84834.1 ATPase, E1-E2 type, Peptidase M, neutral zinc metallopeptidases, zinc-binding site BF325038 Glycine_max_release_2 711165 712911 ATPase = E1-E2 type; Peptidase M = neutral zinc metallopeptidases = zinc- binding site [Medicago truncatula (Barrel medic)] FE897117 Phaseolus_vulgaris 715539 715874 UniRef100_Q93VL6 NBS- LRR resistance-like protein J78 n = 1 Tax = Phaseolus vulgaris RepID = Q93VL6_PHAVU 2.00E−47 TC264844 GMGI.071508 731939 732440 weakly similar to UniRef100_A7PD05 Cluster: Chromosome chr17 scaffold_12 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr17 scaffold_12 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (13%) TA67235_3847 Glycine_max_release_2 731939 733078 NA CD404253 GMGI.071508 732439 733078 homologue to UniRef100_A7PM92 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (8%) BU091162 GMGI.071508 737876 738292 NA BU091162 Glycine_max_release_2 737876 738363 NA asmbl_11870 Vigna_unguiculata 740144 741401 NA BI470779 GMGI.071508 740189 741746 similar to UniRef100_Q9XQB0 Cluster: Carbonic anhydrase; n = 1; Vigna radiata var. radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vigna radiata) = partial (30%) TA43150_3847 Glycine_max_release_2 740126 742524 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] BG509786 GMGI.071508 740265 742434 homologue to UniRef100_Q9XQB0 Cluster: Carbonic anhydrase; n = 1; Vigna radiata var. radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vigna radiata) = partial (34%) BG509786 Glycine_max_release_2 740265 742656 Carbonic anhydrase [Zea mays (Maize)] DT083317 Glycine_soja_release_2 740299 742670 Carbonic anhydrase [Zea mays (Maize)] AW781596 Glycine_max_release_2 740182 742860 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] BU089680 Glycine_max_release_2 741070 742671 Carbonic anhydrase [Zea mays (Maize)] BM887226 Glycine_max_release_2 741037 742852 Carbonic anhydrase [Zea mays (Maize)] BU089600 Glycine_max_release_2 741070 742891 Carbonic anhydrase [Zea mays (Maize)] TC23104 LJGI.070108 740127 744319 similar to UniRef100_Q9XQB0 Cluster: Carbonic anhydrase, n = 1, Vigna radiata var. radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vigna radiata), partial (98%) TA2934_3885 Phaseolus_vulgaris_release_2 739932 744687 Carbonic anhydrase [Zea mays (Maize)] TC238511 GMGI.071508 740118 744639 homologue to UniRef100_Q9XQB0 Cluster: Carbonic anhydrase; n = 1; Vigna radiata var. radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vigna radiata) = complete TA377_34305 Lotus_japonicus_release_1 740127 744704 Carbonic anhydrase [Zea mays (Maize)] Pvcon229 Phaseolus_vulgaris 740125 744728 UniRef100_Q9XQB0 Carbonic anhydrase n = 1 Tax = Vigna radiata var. radiata RepID = Q9XQB0_PHAAU 1.00E−176 TA2935_3885 Phaseolus_vulgaris_release_2 740178 744687 Carbonic anhydrase [Zea mays (Maize)] TA2376_3848 Glycine_soja_release_2 740118 744805 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] TA43157_3847 Glycine_max_release_2 740117 744844 Carbonic anhydrase [Zea mays (Maize)] TA43160_3847 Glycine_max_release_2 741051 744186 Carbonic anhydrase = chloroplast precursor (EC 4.2.1.1) (Carbonate dehydratase) [Contains: Carbonic anhydrase = 27 kDa isoform; Carbonic anhydrase = 25 kDa isoform] [Pisum sativum (Garden pea)] TC135779 MTGI.071708 741364 744530 homologue to UniRef100_P17067 Cluster: Carbonic anhydrase, chloroplast precursor (Carbonate dehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform, Carbonic anhydrase, 25 kDa isoform], n = 1, Pisum sativum|Rep: Carbonic anhydrase, chloroplast precursor (Carbonate dehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform, Carbonic anhydrase, 25 kDa isoform]- Pisum sativum (Garden pea), partial (79%) TA4174_3848 Glycine_soja_release_2 742624 743398 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] Pvcon228 Phaseolus_vulgaris 741374 744687 UniRef100_Q9XQB0 Carbonic anhydrase n = 1 Tax = Vigna radiata var. radiata RepID = Q9XQB0_PHAAU 1.00E−137 TA43163_3847 Glycine_max_release_2 741381 744770 Carbonic anhydrase [Zea mays (Maize)] TC247359 GMGI.071508 741381 744770 homologue to UniRef100_Q9XQB0 Cluster: Carbonic anhydrase; n = 1; Vigna radiata var. radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vigna radiata) = partial (62%) BG045644 Glycine_soja_release_2 742643 743622 Carbonic anhydrase = chloroplast precursor (EC 4.2.1.1) (Carbonate dehydratase) [Contains: Carbonic anhydrase = 27 kDa isoform; Carbonic anhydrase = 25 kDa isoform] [Pisum sativum (Garden pea)] Pvcon227 Phaseolus_vulgaris 741681 744687 UniRef100_Q9XQB0 Carbonic anhydrase n = 1 Tax = Vigna radiata var. radiata RepID = Q9XQB0_PHAAU 1.00E−133 TC124201 MTGI.071708 741922 744665 homologue to UniRef100_P17067 Cluster: Carbonic anhydrase, chloroplast precursor (Carbonate dehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform, Carbonic anhydrase, 25 kDa isoform], n = 1, Pisum sativum|Rep: Carbonic anhydrase, chloroplast precursor (Carbonate dehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform, Carbonic anhydrase, 25 kDa isoform]- Pisum sativum (Garden pea), partial (57%) CB543710 Phaseolus_vulgaris_release_2 742464 744532 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] CB539509 Phaseolus_vulgaris_release_2 742480 744557 Carbonic anhydrase [Zea mays (Maize)] TC126947 MTGI.071708 742434 744665 homologue to UniRef100_P17067 Cluster: Carbonic anhydrase, chloroplast precursor (Carbonate dehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform, Carbonic anhydrase, 25 kDa isoform], n = 1, Pisum sativum|Rep: Carbonic anhydrase, chloroplast precursor (Carbonate dehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform, Carbonic anhydrase, 25 kDa isoform]- Pisum sativum (Garden pea), partial (51%) asmbl_11871 Vigna_unguiculata 742823 744369 NA asmbl_11872 Vigna_unguiculata 742628 744687 NA asmbl_11874 Vigna_unguiculata 742641 744687 NA TA43165_3847 Glycine_max_release_2 742658 744772 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] TC241035 GMGI.071508 742658 744772 homologue to UniRef100_Q9XQB0 Cluster: Carbonic anhydrase; n = 1; Vigna radiata var. radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vigna radiata) = partial (38%) TA480_3888 Pisum_sativum_release_2 742823 744641 Carbonic anhydrase, chloroplast precursor (EC 4.2.1.1) (Carbonate dehydratase) [Contains: Carbonic anhydrase, 27 kDa isoform, Carbonic anhydrase, 25 kDa isoform] [Pisum sativum (Garden pea)] TC240357 GMGI.071508 742650 744828 homologue to UniRef100_Q9XQB0 Cluster: Carbonic anhydrase; n = 1; Vigna radiata var. radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vigna radiata) = partial (38%) BE346766 Glycine_max_release_2 743636 744227 Carbonic anhydrase = chloroplast precursor (EC 4.2.1.1) (Carbonate dehydratase) [Contains: Carbonic anhydrase = 27 kDa isoform; Carbonic anhydrase = 25 kDa isoform] [Pisum sativum (Garden pea)] AW596246 Glycine_max_release_2 743636 744243 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] BE807206 Glycine_max_release_2 743636 744244 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] CB280659 Phaseolus_vulgaris_release_2 743613 744419 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] asmbl_11875 Vigna_unguiculata 743587 744642 NA DT083076 Glycine_soja_release_2 743565 744678 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] TC29040 LJGI.070108 743565 744702 similar to UniRef100_Q9XQB0 Cluster: Carbonic anhydrase, n = 1, Vigna radiata var. radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vigna radiata), partial (31%) TA134_47247 Lotus_corniculatus_release_1 743568 744704 Carbonic anhydrase related cluster TA378_34305 Lotus_japonicus_release_1 743568 744704 Carbonic anhydrase, prokaryotic and plant [Medicago truncatula (Barrel medic)] TC24201 LJGI.070108 743584 744704 similar to UniRef100_Q9XQB0 Cluster: Carbonic anhydrase, n = 1, Vigna radiata var. radiata|Rep: Carbonic anhydrase - Phaseolus aureus (Mung bean) (Vigna radiata), partial (25%) CB539196 Phaseolus_vulgaris_release_2 743626 744687 Carbonic anhydrase [Phaseolus aureus (Mung bean) (Vigna radiata)] AV413187 LJGI.070108 744089 744647 similar to UniRef100_P27140 Cluster: Carbonic anhydrase, chloroplast precursor, n = 4, Arabidopsis thaliana|Rep: Carbonic anhydrase, chloroplast precursor - Arabidopsis thaliana (Mouse-ear cress), partial (17%) AV413187 Lotus_japonicus_release_1 744089 744672 Carbonic anhydrase, chloroplast precursor [Arabidopsis thaliana (Mouse-ear cress)] CD860850 Pisum_sativum_release_2 744145 744641 Carbonic anhydrase, chloroplast precursor [Arabidopsis thaliana (Mouse-ear cress)] CD403834 Glycine_max_release_2 744076 744732 Carbonic anhydrase = chloroplast precursor [Arabidopsis thaliana (Mouse- ear cress)] CD415400 Glycine_max_release_2 744251 744691 NA asmbl_11873 Vigna_unguiculata 744448 744649 NA CB541850 Phaseolus_vulgaris 747218 747570 No significant hit (e−20) BM953717 Glycine_max_release_2 747199 748912 Peptidase S1 and S6 = chymotrypsin/Hap [Medicago truncatula (Barrel medic)] EH256926 GMGI.071508 747192 749279 homologue to UniRef100_A7Q7E6 Cluster: Chromosome chr18 scaffold_59 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr18 scaffold_59 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (21%) TA51716_3847 Glycine_max_release_2 747191 749327 Putative DegP protease [Oryza sativa (japonica cultivar- group)] TC243148 GMGI.071508 747199 749327 homologue to UniRef100_A7Q7E6 Cluster: Chromosome chr18 scaffold_59 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr18 scaffold_59 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (25%) AV768772 LJGI.070108 747281 749288 homologue to UniRef100_O22609 Cluster: Protease Do-like 1, chloroplast precursor, n = 1, Arabidopsis thaliana|Rep: Protease Do-like 1, chloroplast precursor - Arabidopsis thaliana (Mouse- ear cress), partial (23%) BE807421 Glycine_max_release_2 748776 749688 Peptidase S1 and S6 = chymotrypsin/Hap [Medicago truncatula (Barrel medic)] TA51715_3847 Glycine_max_release_2 747251 752927 Peptidase S1 and S6 = chymotrypsin/Hap [Medicago truncatula (Barrel medic)] TC260884 GMGI.071508 747251 752942 homologue to UniRef100_A7Q7E6 Cluster: Chromosome chr18 scaffold_59 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr18 scaffold_59 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (80%) BE474482 Glycine_max_release_2 751068 752387 Peptidase S1 and S6 = chymotrypsin/Hap [Medicago truncatula (Barrel medic)] BE474482 GMGI.071508 751070 752387 homologue to UniRef100_A7Q7E6 Cluster: Chromosome chr18 scaffold_59 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr18 scaffold_59 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (19%) TC261290 GMGI.071508 755656 757218 similar to UniRef100_A7PM96 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (33%) BG646067 MTGI.071708 756996 759297 similar to UniRef100_A7PM96 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (33%) BE555567 Glycine_max_release_2 757210 762134 Hypothetical protein [Medicago truncatula (Barrel medic)] BE555567 GMGI.071508 757746 762134 similar to UniRef100_A7PM96 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (31%) BE058948 Glycine_max_release_2 762117 763784 Hypothetical protein [Medicago truncatula (Barrel medic)] BE058948 GMGI.071508 762818 763784 similar to UniRef100_A7PM96 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (25%) TC138874 MTGI.071708 768876 770881 similar to UniRef100_Q40318 Cluster: Coil protein, n = 1, Medicago sativa|Rep: Coil protein - Medicago sativa (Alfalfa), partial (60%) TC124470 MTGI.071708 768770 771318 similar to UniRef100_Q1RU40 Cluster: Lipolytic enzyme, G- D-S-L, n = 1, Medicago truncatula|Rep: Lipolytic enzyme, G-D-S-L - Medicago truncatula (Barrel medic), partial (77%) TC268582 GMGI.071508 768733 771727 weakly similar to UniRef100_A7PMA0 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (89%) BE059369 Glycine_max_release_2 770328 771326 Lipolytic enzyme = G-D-S-L [Medicago truncatula (Barrel medic)] BE329784 GMGI.071508 770783 771236 similar to UniRef100_Q1RU40 Cluster: Lipolytic enzyme = G- D-S-L; n = 1; Medicago truncatula|Rep: Lipolytic enzyme = G-D-S-L - Medicago truncatula (Barrel medic) = partial (27%) BE329784 Glycine_max_release_2 770783 771288 Lipolytic enzyme = G-D-S-L [Medicago truncatula (Barrel medic)] TA68573_3847 Glycine_max_release_2 773983 774836 Putative kinesin light chain [Oryza sativa (japonica cultivar-group)] TC259227 GMGI.071508 773983 774836 similar to UniRef100_A7PD12 Cluster: Chromosome chr17 scaffold_12 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr17 scaffold_12 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (13%) AI759741 Glycine_max_release_2 774118 774822 Putative kinesin light chain [Oryza sativa (japonica cultivar-group)] asmbl_11876 Vigna_unguiculata 774030 774978 NA TC139308 MTGI.071708 774935 775598 similar to UniRef100_A7PMA1 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (34%) AW186182 Glycine_max_release_2 775276 775796 Similarity to kinesin light chain [Arabidopsis thaliana (Mouse- ear cress)] AW186182 GMGI.071508 775464 775796 similar to UniRef100_A7PD12 Cluster: Chromosome chr17 scaffold_12 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr17 scaffold_12 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (16%) BF010272 GMGI.071508 783671 784035 UniRef100_Q00K67 Cluster: Major surface antigen; n = 1; Hepatitis B virus|Rep: Major surface antigen - Hepatitis B virus (HBV) = partial (5%) TA54422_3847 Glycine_max_release_2 783644 784982 Alcohol dehydrogenase superfamily = zinc-containing [Medicago truncatula (Barrel medic)] BI971258 Glycine_max_release_2 783921 784926 Auxin-induced protein [Vigna radiata] CV542673 Phaseolus_vulgaris_release_2 784213 785346 Quinone oxidoreductase-like protein [Helianthus annuus (Common sunflower)] TC239445 GMGI.071508 783904 786356 similar to UniRef100_O23939 Cluster: Ripening-induced protein; n = 1; Fragaria vesca|Rep: Ripening-induced protein - Fragaria vesca (Woodland strawberry) = partial (84%) TA3037_3848 Glycine_soja_release_2 784204 786191 Quinone oxidoreductase-like protein [Helianthus annuus (Common sunflower)] BG045149 Glycine_soja_release_2 784943 785469 Quinone oxidoreductase [Fragaria ananassa (Strawberry)] TA54423_3847 Glycine_max_release_2 784420 786354 Quinone oxidoreductase-like protein [Helianthus annuus (Common sunflower)] BG046280 Glycine_soja_release_2 786163 786344 NA CA901808 Phaseolus_coccineus_release_2 800890 801759 Alcohol dehydrogenase superfamily, zinc-containing [Medicago truncatula (Barrel medic)] TA14086_34305 Lotus_japonicus_release_1 800932 801745 Alcohol dehydrogenase superfamily, zinc-containing [Medicago truncatula (Barrel medic)] (SEQ ID NO: 15) TC23841 LJGI.070108 800932 801745 similar to UniRef100_Q43677 Cluster: Auxin-induced protein, n = 1, Vigna radiata|Rep: Auxin- induced protein - Vigna radiata, partial (40%) M0093116 SEQ. 805373 805788 SEQ ID NO: 6 Listing TC252650 GMGI.071508 805357 806601 similar to UniRef100_Q43677 Cluster: Auxin-induced protein; n = 1; Vigna radiata|Rep: Auxin- induced protein - Vigna radiata = partial (54%) BARC-039375- ePCR&blat 805660 806532 Map3.0 SNP L/Gm19 cM: 3.4 07304 TA65006_3847 Glycine_max_release_2 805357 807089 Quinone oxidoreductase-like protein [Helianthus annuus (Common sunflower)] TA65005_3847 Glycine_max_release_2 806611 807310 Alcohol dehydrogenase superfamily = zinc-containing [Medicago truncatula (Barrel medic)] TC274718 GMGI.071508 806611 807310 similar to UniRef100_Q43677 Cluster: Auxin-induced protein; n = 1; Vigna radiata|Rep: Auxin- induced protein - Vigna radiata = partial (30%) AW397551 Glycine_max_release_2 811245 811796 Auxin-induced protein [Vigna radiata] Pvcon4580 Phaseolus_vulgaris 811330 813524 UniRef100_Q43677 Auxin- induced protein n = 1 Tax = Vigna radiata RepID = Q43677_9FABA 1.00E−133 asmbl_11877 Vigna_unguiculata 812523 812779 NA BE608172 Glycine_max_release_2 821487 822389 Protein farnesyltransferase subunit beta [Pisum sativum (Garden pea)] BQ273477 Glycine_max_release_2 821559 822383 NA TC246895 GMGI.071508 821516 822443 similar to UniRef100_Q04903 Cluster: Protein farnesyltransferase subunit beta; n = 1; Pisum sativum|Rep: Protein farnesyltransferase subunit beta - Pisum sativum (Garden pea) = partial (15%) TC241767 GMGI.071508 824186 828116 similar to UniRef100_Q7XHJ0 Cluster: Formate dehydrogenase; n = 1; Quercus robur|Rep: Formate dehydrogenase - Quercus robur (English oak) = partial (97%) TA40711_3847 Glycine_max_release_2 824209 828372 Formate dehydrogenase [Quercus robur (English oak)] AI522957 Glycine_max_release_2 826883 827087 Formate dehydrogenase [Quercus robur (English oak)] BG044450 Glycine_soja_release_2 826544 827461 Formate dehydrogenase = mitochondrial precursor [Solanum tuberosum (Potato)] asmbl_11878 Vigna_unguiculata 826586 827463 NA CA800817 Glycine_soja_release_2 826705 827869 Formate dehydrogenase [Quercus robur (English oak)] TC240429 GMGI.071508 826957 828379 similar to UniRef100_Q9ZRI8 Cluster: Formate dehydrogenase = mitochondrial precursor; n = 1; Hordeum vulgare|Rep: Formate dehydrogenase = mitochondrial precursor - Hordeum vulgare (Barley) = partial (40%) AW350528 Glycine_max_release_2 826986 828379 Formate dehydrogenase 1 = mitochondrial precursor [Oryza sativa (Rice)] BG882062 Glycine_max_release_2 827372 828284 Formate dehydrogenase 1 = mitochondrial precursor [Oryza sativa (Rice)] BE347639 Glycine_max_release_2 827443 828262 Formate dehydrogenase 1 = mitochondrial precursor [Oryza sativa (Rice)] CA782711 Glycine_soja_release_2 827371 828357 Formate dehydrogenase 1 = mitochondrial precursor [Oryza sativa (Rice)] TA40821_3847 Glycine_max_release_2 829640 832253 Formate dehydrogenase [Quercus robur (English oak)] BE330555 Glycine_max_release_2 829875 832057 Formate dehydrogenase = mitochondrial precursor [Solanum tuberosum (Potato)] BU090495 Glycine_max_release_2 829863 832082 Formate dehydrogenase [Quercus robur (English oak)] BG044406 Glycine_soja_release_2 829915 832082 Formate dehydrogenase [Quercus robur (English oak)] AW508186 GMGI.071508 830914 831336 similar to UniRef100_A7PMA5 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (15%) M0129925 SEQ 830552 831704 SEQ ID NO: 7 LISTING AW508186 Glycine_max_release_2 830914 831970 Formate dehydrogenase = mitochondrial precursor [Solanum tuberosum (Potato)] AW508145 Glycine_max_release_2 830909 832061 Formate dehydrogenase [Quercus robur (English oak)] TA40373_3847 Glycine_max_release_2 830863 832118 Formate dehydrogenase [Quercus robur (English oak)] AW397259 Glycine_max_release_2 831219 832141 Formate dehydrogenase [Quercus robur (English oak)] TC261330 GMGI.071508 829795 833576 similar to UniRef100_Q7XHJ0 Cluster: Formate dehydrogenase; n = 1; Quercus robur|Rep: Formate dehydrogenase - Quercus robur (English oak) = partial (96%) TC249502 GMGI.071508 830866 832529 similar to UniRef100_Q7XHJ0 Cluster: Formate dehydrogenase; n = 1; Quercus robur|Rep: Formate dehydrogenase - Quercus robur (English oak) = partial (72%) TA40376_3847 Glycine_max_release_2 830879 833356 Formate dehydrogenase [Quercus robur (English oak)] asmbl_11879 Vigna_unguiculata 831735 833050 NA AW569072 GMGI.071508 832471 832890 similar to UniRef100_Q7XHJ0 Cluster: Formate dehydrogenase; n = 1; Quercus robur|Rep: Formate dehydrogenase - Quercus robur (English oak) = partial (9%) AW569072 Glycine_max_release_2 832471 832929 Formate dehydrogenase [Quercus robur (English oak)] TA40339_3847 Glycine_max_release_2 832130 833531 Formate dehydrogenase 1 = mitochondrial precursor [Oryza sativa (Rice)] TA5191_3885 Phaseolus_vulgaris_release_2 832192 833517 Formate dehydrogenase [Quercus robur (English oak)] FD790937 Phaseolus_vulgaris 833039 833412 UniRef100_A6N0B2 Mitochondrial formate dehydrogenase 1 (Fragment) n = 1 Tax = Oryza sativa Indica Group RepID = A6N0B2_ORYSI 3.00E−30 CA913454 Phaseolus_coccineus_release_2 841331 841722 NA TA70199_3847 Glycine_max_release_2 841305 841824 NA asmbl_11880 Vigna_unguiculata 841326 841889 NA TA3611_3848 Glycine_soja_release_2 841347 842640 Hypothetical protein OJ1593_C11.11 [Oryza sativa (japonica cultivar-group)] TA5381_34305 Lotus_japonicus_release_1 841455 842700 Calcium homeostasis regulator CHoR1 [Solanum tuberosum (Potato)] TC20706 LJGI.070108 841455 842700 weakly similar to UniRef100_Q5QTN8 Cluster: Calcium homeostasis regulator CHoR1, n = 1, Solanum tuberosum|Rep: Calcium homeostasis regulator CHoR1 - Solanum tuberosum (Potato), partial (52%) Pvcon2378 Phaseolus_vulgaris 841347 843522 UniRef100_A7PMA9 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMA9_VITVI 4.00E−94 TC252755 GMGI.071508 841305 843655 similar to UniRef100_A7PMA9 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (74%) EX305183 Phaseolus_vulgaris 841682 843613 UniRef100_A7PMA9 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMA9_VITVI 1.00E−67 BI498351 GMGI.071508 844582 845168 NA TA66563_3847 Glycine_max_release_2 844582 847078 Hypothetical protein [Ipomoea trifida (Morning glory)] TC247953 GMGI.071508 844582 847220 similar to UniRef100_A7Q5T8 Cluster: Chromosome chr14 scaffold_54 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_54 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (58%) TA3593_3848 Glycine_soja_release_2 844668 847194 Hypothetical protein [Ipomoea trifida (Morning glory)] TA56324_3847 Glycine_max_release_2 854425 856413 Similarity to intracellular protein [Arabidopsis thaliana (Mouse-ear cress)] TC235843 GMGI.071508 854425 856413 similar to UniRef100_A7PMB1 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (40%) CD406351 Glycine_max_release_2 855627 856402 Similarity to intracellular protein [Arabidopsis thaliana (Mouse-ear cress)] TC276442 GMGI.071508 855627 856402 similar to UniRef100_A7PMB1 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (14%) TC273993 GMGI.071508 863632 864262 homologue to UniRef100_A7PMB2 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (26%) BU082700 Glycine_max_release_2 863841 864449 Hypothetical protein OJ1126_B10.9 [Oryza sativa (japonica cultivar-group)] (SEQ ID NO: 14) AW459960 Glycine_max_release_2 863632 865288 Hypothetical protein F4P13.4 [Arabidopsis thaliana (Mouse- ear cress)] AL385435 MTGI.071708 863952 865397 homologue to UniRef100_A7PD25 Cluster: Chromosome chr17 scaffold_12, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr17 scaffold_12, whole genome shotgun sequence - Vitis vinifera (Grape), partial (37%) AI856244 GMGI.071508 864500 864958 UniRef100_A7PMB2 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (6%) asmbl_11881 Vigna_unguiculata 863829 865710 NA TC238318 GMGI.071508 863970 865869 homologue to UniRef100_A7PMB2 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (34%) TA63907_3847 Glycine_max_release_2 864500 865869 Hypothetical protein F4P13.4 [Arabidopsis thaliana (Mouse- ear cress)] BW598574 LJGI.070108 865265 865656 similar to UniRef100_Q8LES3 Cluster: Protein kinase, n = 1, Arabidopsis thaliana|Rep: Protein kinase - Arabidopsis thaliana (Mouse-ear cress), partial (9%) BW598574 Lotus_japonicus_release_1 865265 865674 Protein kinase [Arabidopsis thaliana (Mouse-ear cress)] CD400016 Glycine_max_release_2 870972 871184 NA CD399245 Glycine_max_release_2 870876 871427 Putative Peptidyl-prolyl cis- trans isomerase = chloroplast [Oryza sativa (japonica cultivar-group)] TC242592 GMGI.071508 870943 872827 similar to UniRef100_A6MZC4 Cluster: Peptidyl-prolyl cis- trans isomerase; n = 2; Oryza sativa|Rep: Peptidyl-prolyl cis- trans isomerase - Oryza sativa subsp. indica (Rice) = partial (60%) CB543642 Phaseolus_vulgaris_release_2 871229 872777 Peptidyl-prolyl cis trans isomerase = chloroplast precursor [Spinacia oleracea (Spinach)] TA52959_3847 Glycine_max_release_2 870943 873450 Poly(A) polymerase [Pisum sativum (Garden pea)] CB539263 Phaseolus_vulgaris_release_2 871195 873325 Poly(A) polymerase [Pisum sativum (Garden pea)] Pvcon1578 Phaseolus_vulgaris 870946 876143 UniRef100_O22636 Poly(A) polymerase n = 1 Tax = Pisum sativum RepID = O22636_PEA E-0 TA10487_34305 Lotus_japonicus_release_1 873266 875963 Poly(A) polymerase [Pisum sativum (Garden pea)] TA6667_47247 Lotus_corniculatus_release_1 873266 875963 Poly(A) polymerase related cluster TC34747 LJGI.070108 873266 875963 similar to UniRef100_O22636 Cluster: Poly(A) polymerase, n = 1, Pisum sativum|Rep: Poly(A) polymerase - Pisum sativum (Garden pea), partial (57%) BG363373 Glycine_max_release_2 874357 874944 Poly(A) polymerase [Pisum sativum (Garden pea)] TC251420 GMGI.071508 874369 876078 similar to UniRef100_O22636 Cluster: Poly(A) polymerase; n = 1; Pisum sativum|Rep: Poly(A) polymerase - Pisum sativum (Garden pea) = partial (37%) CA901088 Phaseolus_coccineus_release_2 874490 876191 Poly(A) polymerase [Pisum sativum (Garden pea)] asmbl_11882 Vigna_unguiculata 886629 890018 NA TA68870_3847 Glycine_max_release_2 886534 893419 Senescence-associated protein- like [Oryza sativa (japonica cultivar-group)] TC270337 GMGI.071508 886672 893419 weakly similar to UniRef100_A7PD28 Cluster: Chromosome chr17 scaffold_12 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr17 scaffold_12 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (86%) M0205537 SEQ. 890458 890051 SEQ ID NO: 8 Listing BM732054 Glycine_max_release_2 899859 901015 NA BM732054 GMGI.071508 900006 901015 similar to UniRef100_Q04TD2 Cluster: MviN-related protein; n = 1; Leptospira borgpetersenii serovar Hardjo-bovis JB197|Rep: = partial (2%) toGm13 DAGchainer 816170 1014875 Ks0.1202 M0202715 SEQ. 921233 921630 SEQ ID NO: 9 Listing TA46168_3847 Glycine_max_release_2 921047 924660 Homeodomain leucine zipper protein HDZ3 [Phaseolus vulgaris (Kidney bean) (French bean)] TC260016 GMGI.071508 921056 924739 homologue to UniRef100_Q93XA3 Cluster: Homeodomain leucine zipper protein HDZ3; n = 1; Phaseolus vulgaris|Rep: Homeodomain leucine zipper protein HDZ3 - Phaseolus vulgaris (Kidney bean) (French bean) = complete Pvcon1101 Phaseolus_vulgaris 921086 924758 UniRef100_Q93XA3 Homeodomain leucine zipper protein HDZ3 (Fragment) n = 1 Tax = Phaseolus vulgaris RepID = Q93XA3_PHAVU 1.00E−124 TA3604_3885 Phaseolus_vulgaris_release_2 921111 924754 Homeodomain leucine zipper protein HDZ3 [Phaseolus vulgaris (Kidney bean) (French bean)] asmbl_11883 Vigna_unguiculata 921538 924758 NA BG041631 Glycine_soja_release_2 923015 923340 Homeobox-leucine zipper protein HAT5 [Arabidopsis thaliana (Mouse-ear cress)] AV421688 LJGI.070108 923118 924180 similar to UniRef100_Q93XA3 Cluster: Homeodomain leucine zipper protein HDZ3, n = 1, Phaseolus vulgaris|Rep: Homeodomain leucine zipper protein HDZ3 - Phaseolus vulgaris (Kidney bean) (French bean), partial (25%) TC235979 GMGI.071508 923000 924768 similar to UniRef100_Q93XA3 Cluster: Homeodomain leucine zipper protein HDZ3; n = 1; Phaseolus vulgaris|Rep: Homeodomain leucine zipper protein HDZ3 - Phaseolus vulgaris (Kidney bean) (French bean) = partial (86%) TA46165_3847 Glycine_max_release_2 923000 924779 Homeodomain leucine zipper protein HDZ3 [Phaseolus vulgaris (Kidney bean) (French bean)] AW351287 Glycine_max_release_2 923128 924720 Homeodomain leucine zipper protein HDZ3 [Phaseolus vulgaris (Kidney bean) (French bean)] CA785782 Glycine_soja_release_2 925713 925880 NA Pvcon8364 Phaseolus_vulgaris 925735 926609 UniRef100_A7PMB7 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMB7_VITVI 1.00E−27 BE248998 MTGI.071708 926978 927524 similar to UniRef100_Q7F8S7 Cluster: PHD finger-like protein, n = 1, Oryza sativa Japonica Group|Rep: PHD finger-like protein - Oryza sativa subsp. japonica (Rice), partial (4%) TC35470 LJGI.070108 928423 929804 similar to UniRef100_A7PMB8 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (9%) TA11035_34305 Lotus_japonicus_release_1 928423 929825 PHD finger-like protein [Oryza sativa (japonica cultivar- group)] CA911004 Phaseolus_coccineus_release_2 934882 939256 T13O15.10 protein [Arabidopsis thaliana (Mouse- ear cress)] AI856399 GMGI.071508 937577 938041 NA AI856399 Glycine_max_release_2 937577 938106 NA AW348703 Glycine_max_release_2 963043 963750 NA TC276191 GMGI.071508 963049 964044 weakly similar to UniRef100_A7PZY3 Cluster: Chromosome chr8 scaffold_41 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr8 scaffold_41 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (21%) BQ628183 Glycine_max_release_2 963625 964044 NA BQ080193 Glycine_max_release_2 963695 967475 NA TA52645_3847 Glycine_max_release_2 963720 967461 NA TC256882 GMGI.071508 963774 967475 weakly similar to UniRef100_A7PZY3 Cluster: Chromosome chr8 scaffold_41 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr8 scaffold_41 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (45%) BG156825 Glycine_max_release_2 971121 971284 NA BG156825 GMGI.071508 971125 971284 NA BU545761 Glycine_max_release_2 971300 971901 NA BU550718 Glycine_max_release_2 971255 973578 NA TA72701_3847 Glycine_max_release_2 972120 972806 NA TC271942 GMGI.071508 972201 972806 NA TC269989 GMGI.071508 971255 973827 similar to UniRef100_A7P2M9 Cluster: Chromosome chr1 scaffold_5 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr1 scaffold_5 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (63%) BI317782 Glycine_max_release_2 971510 973827 NA BI893512 Glycine_max_release_2 971537 973848 NA BI893512 GMGI.071508 971671 973848 similar to UniRef100_A7P2M9 Cluster: Chromosome chr1 scaffold_5 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr1 scaffold_5 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (54%) CO985587 Glycine_max_release_2 974859 976255 Putative GTP-binding membrane protein LepA [Oryza sativa (japonica cultivar- group)] AW596868 Glycine_max_release_2 976346 976856 NA AW596868 GMGI.071508 976412 976856 similar to UniRef100_A2Q5T1 Cluster: Tetratricopeptide-like helical; n = 1; Medicago truncatula|Rep: Tetratricopeptide-like helical - Medicago truncatula (Barrel medic) = partial (5%) CA901672 Phaseolus_coccineus_release_2 983905 984264 Aldehyde dehydrogenase 1 precursor [Lotus corniculatus (Bird's-foot trefoil)] WmFPC_Contig4169 899736 1068750 NA FE898889 Phaseolus_vulgaris 983908 984989 UniRef100_A7PD33 Chromosome chr17 scaffold_12, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PD33_VITVI 2.00E−79 TC273361 GMGI.071508 984396 986122 similar to UniRef100_P93344 Cluster: Aldehyde dehydrogenase; n = 1; Nicotiana tabacum|Rep: Aldehyde dehydrogenase - Nicotiana tabacum (Common tobacco) = partial (37%) BE473475 Glycine_max_release_2 984960 986122 Aldehyde dehydrogenase [Nicotiana tabacum (Common tobacco)] CV539672 Phaseolus_vulgaris 985959 987101 UniRef100_P93344 Aldehyde dehydrogenase (NAD+) n = 1 Tax = Nicotiana tabacum RepID = P93344_TOBAC 7.00E−50 AV410805 LJGI.070108 987592 987888 similar to UniRef100_A7PMC7 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (6%) TC265505 GMGI.071508 1011306 1012664 similar to UniRef100_A7PMD1 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (28%) TA51641_3847 Glycine_max_release_2 1011306 1013783 Putative high-affinity potassium transporter protein 1 [Nicotiana tabacum (Common tobacco)] CB540416 Phaseolus_vulgaris 1012333 1013531 UniRef100_A7PMD1 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMD1_VITVI 5.00E−97 BM891067 GMGI.071508 1012675 1013617 similar to UniRef100_A7PMD1 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (22%) TC131883 MTGI.071708 1012665 1014070 similar to UniRef100_A7PMD1 Cluster: Chromosome chr14 scaffold_21, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr14 scaffold_21, whole genome shotgun sequence - Vitis vinifera (Grape), partial (34%) asmbl_11884 Vigna_unguiculata 1012674 1014123 NA BE330787 Glycine_max_release_2 1013888 1014305 Putative high-affinity potassium transporter protein [Phytolacca esculenta (Food pokeberry)] FD792954 Phaseolus_vulgaris 1013779 1014573 UniRef100_A7PMD1 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMD1_VITVI 3.00E−57 TC244134 GMGI.071508 1014004 1014793 similar to UniRef100_A7PMD1 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (15%) TA51642_3847 Glycine_max_release_2 1013926 1014875 Putative high-affinity potassium transporter 1 [Nicotiana rustica (Aztec tobacco)] TC242106 GMGI.071508 1013926 1014875 similar to UniRef100_A7PMD1 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (15%) BI970123 Glycine_max_release_2 1014128 1014721 Putative potassium transporter HAK1p [Mesembryanthemum crystallinum (Common ice plant)] BQ080303 Glycine_max_release_2 1018604 1019142 NA TC270109 GMGI.071508 1018604 1019142 weakly similar to UniRef100_UPI0000196D39 Cluster: NHL repeat-containing protein; n = 1; Arabidopsis thaliana|Rep: NHL repeat- containing protein - Arabidopsis thaliana = partial (4%) BQ080219 Glycine_max_release_2 1018604 1019579 NA TA62145_3847 Glycine_max_release_2 1021347 1023221 NA TC245123 GMGI.071508 1021347 1023221 similar to UniRef100_A7PMD2 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (31%) asmbl_11885 Vigna_unguiculata 1022417 1022510 NA CA784724 Glycine_max_release_2 1046117 1047384 NA CA784724 GMGI.071508 1046400 1047384 similar to UniRef100_A7Q2E7 Cluster: Chromosome chr1 scaffold_46 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr1 scaffold_46 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (17%) Pvcon4015 Phaseolus_vulgaris 1047011 1048610 UniRef100_A5ATC1 Putative uncharacterized protein n = 1 Tax = Vitis vinifera RepID = A5ATC1_VITVI 1.00E−146 BQ742289 Glycine_max_release_2 1048650 1048767 NA BF068315 GMGI.071508 1057203 1057316 similar to UniRef100_Q8MIG1 Cluster: Skinkine; n = 1; Sus scrofa|Rep: Skinkine - Sus scrofa (Pig) = partial (12%) BF068315 Glycine_max_release_2 1057203 1057506 NA BU083500 GMGI.071508 1058026 1058431 UniRef100_Q2R023 Cluster: Expressed protein; n = 1; Oryza sativa Japonica Group|Rep: Expressed protein - Oryza sativa = partial (2%) TA74227_3847 Glycine_max_release_2 1058026 1059408 NA BI423963 GMGI.071508 1058432 1059275 similar to UniRef100_Q2QDD6 Cluster: Nodulin-like protein; n = 1; Gossypium hirsutum|Rep: Nodulin-like protein - Gossypium hirsutum (Upland cotton) (Gossypium mexicanum) = partial (22%) TC237120 GMGI.071508 1063015 1063972 UniRef100_Q39819 Cluster: Hsp22.3; n = 1; Glycine max|Rep: Hsp22.3 - Glycine max (Soybean) = complete CA802234 Glycine_soja_release_2 1061477 1067499 Similarity to nodulin [Arabidopsis thaliana (Mouse- ear cress)] BI425574 GMGI.071508 1065519 1066854 weakly similar to UniRef100_A7PMD8 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (21%) BI425574 Glycine_max_release_2 1065519 1066940 Hypothetical protein [Medicago truncatula (Barrel medic)] AU251786 LJGI.070108 1066790 1067424 weakly similar to UniRef100_A7Q2G7 Cluster: Chromosome chr1 scaffold_46, whole genome shotgun sequence, n = 1, Vitis vinifera|Rep: Chromosome chr1 scaffold_46, whole genome shotgun sequence - Vitis vinifera (Grape), partial (7%) Pvcon8451 Phaseolus_vulgaris 1065511 1068752 UniRef100_A7PMD8 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMD8_VITVI 7.00E−91 TC260900 GMGI.071508 1065796 1069134 weakly similar to UniRef100_A7PMD8 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (41%) TA63020_3847 Glycine_max_release_2 1067436 1069134 NA CA783703 Glycine_soja_release_2 1068257 1068879 NA TA58065_3847 Glycine_max_release_2 1074998 1076541 AT3g28050/MMG15_6 [Arabidopsis thaliana (Mouse- ear cress)] TC251785 GMGI.071508 1074998 1076541 similar to UniRef100_Q8L9I2 Cluster: Nodulin MtN21-like protein; n = 1; Arabidopsis thaliana|Rep: Nodulin MtN21- like protein - Arabidopsis thaliana (Mouse-ear cress) = partial (16%) CB280623 Phaseolus_vulgaris_release_2 1075036 1076540 AT3g28050/MMG15_6 [Arabidopsis thaliana (Mouse- ear cress)] EH043320 Arachis_stenosperma_release_5 1075056 1077422 Cluster: Hypothetical protein, n = 1, Medicago truncatula|Rep: Hypothetical protein - Medicago truncatula (Barrel medic) asmbl_11886 Vigna_unguiculata 1075036 1077585 NA BQ094260 Glycine_max_release_2 1075548 1077551 Nodulin-like protein [Arabidopsis thaliana (Mouse- ear cress)] BF598290 Glycine_soja_release_2 1075557 1077593 Nodulin-like protein [Arabidopsis thaliana (Mouse- ear cress)] Pvcon6314 Phaseolus_vulgaris 1075036 1078733 UniRef100_A7PMD8 Chromosome chr14 scaffold_21, whole genome shotgun sequence n = 1 Tax = Vitis vinifera RepID = A7PMD8_VITVI 1.00E−105 TA58064_3847 Glycine_max_release_2 1075337 1079189 AT3g28050/MMG15_6 [Arabidopsis thaliana (Mouse- ear cress)] TC255833 GMGI.071508 1075337 1079189 weakly similar to UniRef100_A7PMD8 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (64%) BG042956 Glycine_soja_release_2 1078885 1079014 NA TC263589 GMGI.071508 1086875 1091139 similar to UniRef100_A7PME0 Cluster: Chromosome chr14 scaffold_21 = whole genome shotgun sequence; n = 1; Vitis vinifera|Rep: Chromosome chr14 scaffold_21 = whole genome shotgun sequence - Vitis vinifera (Grape) = partial (35%) TA50577_3847 Glycine_max_release_2 1086875 1094082 Alpha-dioxygenase [Pisum sativum (Garden pea)] asmbl_11887 Vigna_unguiculata 1089135 1092345 NA CA410123 Lupinus_albus_release_2 1092182 1092694 Alpha-dioxygenase [Pisum sativum (Garden pea)] Pvcon4974 Phaseolus_vulgaris 1091225 1093836 UniRef100_Q5GQ66 Alpha- dioxygenase n = 1 Tax = Pisum sativum RepID = Q5GQ66_PEA E-0 TC243973 GMGI.071508 1091177 1094141 similar to UniRef100_Q5GQ66 Cluster: Alpha-dioxygenase; n = 1; Pisum sativum|Rep: Alpha-dioxygenase - Pisum sativum (Garden pea) = partial (61%) asmbl_11888 Vigna_unguiculata 1092518 1093829 NA M0206054 SEQ. Listing 1465522 1465187 SEQ ID NO: 11 M0205375 SEQ. Listing 2010060 2009541 SEQ ID NO: 12 toGm13 DAGchainer 1046081 4647877 Ks0.2059 NA Glyma1 1 50600000 NA

Sequences for the genes provided above can be obtained from the World Wide Web (or Internet) using the identifiers provided in Column 1 (Locus/Display Name) or Column 5 (ADDITIONAL LOCUS INFORMATION) from the following internet locations:

a) “soybase.org” (described in Grant et al., Nucleic Acids Research, 2010, Vol. 38, Database issue D843-D846) or soybase.org/gbrowse/cgi-bin/gbrowse/gmax1.01/(see Hyten DL, Choi I-Y, Song Q, Specht J E, Carter T E et al. (2010) A high density integrated genetic linkage map of soybean and the development of a 1,536 Universal Soy Linkage Panel for QTL mapping. Crop Science 50:960-968. (Crop Science); and Hyten DL, Cannon SB, Song Q, Weeks N, Fickus E W et al. (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11(1): 38);

b) “phytozome.net” or “phytozome.net/cgi-bin/gbrowse/soybean/?name=Gm09”;

c) “plantgdb.org” or “plantgdb.org/GmGDB/(Assembly version Glyrna1.170 (April 2009)”; and,

d) “ncbi.nlm.nih.gov/sites/entrez” and subsites “ncbi.nlm.nih.gov/nucest”, “ncbi.nlm.nih.gov/dbEST”, “ncbi.nlm.nih.gov/genbank/”, “.ncbi.nlm.nih.gov/sites/genome”, “ncbi.nlm.nih.gov/unigene”, and “ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=3847”. 

We claim:
 1. A method of identifying a soybean plant that comprises a genotype associated with a no flash phenotype, comprising: detecting in said soybean plant a DNA polymorphism in at least one yellow flash marker locus associated with the no flash phenotype with a nucleic acid analysis technique, wherein the yellow flash marker locus is in a linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO:14), and selecting said plant from a population of plants, wherein the selected plant comprises a genotype associated with a no flash phenotype and wherein the selected plant or progeny thereof exhibit a no flash phenotype.
 2. The method of claim 1, wherein said selected plant or progeny thereof comprises a transgene that confers tolerance to glyphosate.
 3. The method of claim 2, wherein said soybean plant or progeny thereof is exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety.
 4. The method of claim 1, wherein said genotype associated with a no flash phenotype is detected by identifying at least one polymorphic allele of at least one marker in a first sub-region of said linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16) and/or at least one polymorphic allele of at least one marker in a second sub-region of said linkage group L region that is flanked by loci TA14086_(—)34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14) with the nucleic acid analysis technique.
 5. The method of claim 1, wherein said genotype associated with a no flash phenotype is detected by identifying at least one polymorphic allele of at least one marker in said linkage group L region selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7) that is associated with a no flash phenotype with the nucleic acid analysis technique.
 6. A method for obtaining a soybean plant comprising in its genome at least one no flash locus, comprising the steps of: a. genotyping a plurality of soybean plants with respect to at least one yellow flash locus in a first linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO:14), wherein said plurality of soybean plants comprises a population that is obtained by: i) crossing a parent plant comprising at least one no flash locus with a parent plant comprising at least one yellow flash locus; or, ii) obtaining seed or progeny from a parental plant segregating for at least one no flash locus; and b. selecting a soybean plant comprising in its genome at least one no flash locus comprising a genotype associated with no flash phenotype, wherein the selected plant exhibits a no flash phenotype.
 7. The method of claim 6, wherein said genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in a first sub-region of said linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16); and/or at least one polymorphic allele of at least one marker in a second sub-region of said linkage group L region that is flanked by loci TA14086_(—)34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14).
 8. The method of claim 6, wherein said genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in said first linkage group L region, said first sub-region, or said second sub-region, wherein said marker is selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7).
 9. The method of claim 6, wherein said plurality of soybean plants comprises a population that is obtained from seed or progeny from a parental plant segregating for at least one no flash locus.
 10. The method of claim 6, wherein said population contains plants that comprise a transgene that confers tolerance to glyphosate.
 11. The method of claim 6, further comprising the step of assaying for the presence of at least one additional marker, wherein said additional marker is either linked or unlinked to said linkage group L genomic region.
 12. The method of claim 6, wherein said plurality of soybean plants, said soybean plant, and/or progeny thereof are exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety.
 13. A method for producing a soybean plant comprising in its genome at least one introgressed no flash locus, comprising the steps of: a. crossing a first no flash soybean plant with a second soybean plant, wherein the second soybean plant comprises a yellow flash locus in a first linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) and at least one linked polymorphic locus not present in said first no flash soybean plant, to obtain a population segregating for the no flash loci and said linked polymorphic locus; b. detecting at least two polymorphic nucleic acids in a seed or progeny plant from at least one soybean plant from said population, wherein at least one of said polymorphic nucleic acids is located in said first linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) and wherein at least one of said polymorphic nucleic acids is in a linked polymorphic locus not present in said first no flash soybean plant; and c. selecting a seed or progeny soybean plant from step b by its genotype, wherein the selected seed or progeny soybean plant comprises a genotype of the first linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) that is associated with a no flash phenotype and at least one linked marker found in said second soybean plant comprising a yellow flash locus but not in said first no flash soybean plant, thereby obtaining a selected soybean plant comprising in its genome at least one introgressed no flash locus.
 14. The method of claim 13, wherein at least one of said first or said second soybean plants comprises a transgene that confers tolerance to glyphosate.
 15. The method of claim 14, wherein said population, said selected soybean plant, and/or progeny of said selected soybean plant is exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety.
 16. The method of claim 13, wherein said yellow flash locus comprises at least one polymorphic allele of at least one marker in a first sub-region of said linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16); and/or at least one polymorphic allele of at least one marker in a second sub-region of said linkage group L region that is flanked by loci TA14086_(—)34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14).
 17. The method of claim 16, wherein said polymorphic nucleic acid located in said first sub-region and/or said second sub-region is detected in step (b) with at least one marker selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7).
 18. The method of claim 17, wherein said polymorphic nucleic acid located in said first sub-region and/or said second sub-region is detected in step (b) with at least one marker selected from the group consisting of M0101742 (SEQ ID NO:5) and M0129925 (SEQ ID NO:7).
 19. The method of claim 17, wherein said polymorphic nucleic acids are detected with marker M0101742 (SEQ ID NO:5) and with marker M0129925 (SEQ ID NO:7).
 20. The method of claim 13, wherein said linked polymorphic locus is detected with a genotypic marker, a phenotypic marker, or both.
 21. The method of claim 13, wherein said linked polymorphic locus is detected with a marker that is located within about 1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) of said no flash locus.
 22. The method of claim 21, wherein said linked polymorphic locus is detected with at least one marker selected from the group consisting of M0205928 (SEQ ID NO:3), M0205537 (SEQ ID NO:8), M0202715 (SEQ ID NO:9), M0206286 (SEQ ID NO:10), M0206054 (SEQ ID NO:11) and M0205375 (SEQ ID NO:12).
 23. A selected soybean plant produced by the method of claim 13 that comprises the introgressed no flash locus from the first no flash soybean plant and one or more polymorphic loci comprising alleles or combinations of alleles that are not found in the first no flash soybean plant, that are linked to said introgressed no flash locus, and are found in the second soybean plant comprising a yellow flash locus, wherein at least 75% of genomic sequences in said selected plant have markers characteristic of soybean germplasm that comprise a genomic region associated with a yellow flash phenotype.
 24. The selected soybean plant of claim 23, wherein said introgressed no flash locus comprises at least one polymorphic allele of at least one marker selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7) that is associated with a no flash phenotype.
 25. The selected soybean plant of claim 24, wherein said polymorphic alleles associated with a no flash phenotype comprise: (i) GG alleles at nucleotide 218 of SEQ ID NO:4, TT alleles at nucleotide 1206 of SEQ ID NO:5, AA alleles at nucleotide 183 of SEQ ID NO:6, and CC alleles at nucleotide 328 of SEQ ID NO:7; or, (ii) AA alleles at nucleotide 218 of SEQ ID NO:4, CC alleles at nucleotide 1206 of SEQ ID NO:5, TT alleles at nucleotide 183 of SEQ ID NO:6, and GG alleles at nucleotide 328 of SEQ ID NO:7.
 26. The selected soybean plant of claim 24, wherein said one or more polymorphic loci comprising alleles or combinations of alleles that are not found in a no flash soybean variety are located within about 1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) of said introgressed no flash locus.
 27. The selected soybean plant of claim 24, wherein said one or more polymorphic loci comprise an allele that are not found in a no flash soybean variety that is detectable with at least one marker selected from the group consisting of M0205928 (SEQ ID NO:3), M0205537 (SEQ ID NO:8), M0202715 (SEQ ID NO:9), M0206286 (SEQ ID NO:10), M0206054 (SEQ ID NO:11) and M0205375 (SEQ ID NO:12).
 28. The method of claim 5, wherein said genotype associated with a no flash phenotype is detected by identifying at least one of: GG or AA alleles at nucleotide 218 of SEQ ID NO:4, TT or CC alleles at nucleotide 1206 of SEQ ID NO:5, AA or TT alleles at nucleotide 183 of SEQ ID NO:6, and/or CC or GG alleles at nucleotide 328 of SEQ ID NO:7 with the nucleic acid analysis technique.
 29. The method of claim 5, wherein said genotype associated with a no flash phenotype is detected by identifying: (i) GG alleles at nucleotide 218 of SEQ ID NO:4, TT alleles at nucleotide 1206 of SEQ ID NO:5, AA alleles at nucleotide 183 of SEQ ID NO:6, and CC alleles at nucleotide 328 of SEQ ID NO:7 with the nucleic acid analysis technique; or, (ii) AA alleles at nucleotide 218 of SEQ ID NO:4, CC alleles at nucleotide 1206 of SEQ ID NO:5, TT alleles at nucleotide 183 of SEQ ID NO:6, and GG alleles at nucleotide 328 of SEQ ID NO:7 with the nucleic acid analysis technique.
 30. The selected soybean plant of claim 23, wherein at least 90% of genomic sequences in said selected plant have markers characteristic of soybean germplasm that comprise a genomic region associated with a yellow flash phenotype.
 31. The selected soybean plant of claim 23, wherein at least 99% of genomic sequences in said selected plant have markers characteristic of soybean germplasm that comprise a genomic region associated with a yellow flash phenotype. 